After the leadership of the Major League Baseball players’ union voted, 26-12, to approve a new labor deal on Thursday afternoon — following years of building mistrust of management and months of tense negotiating — M.L.B.’s commissioner, Rob Manfred, picked up the phone.

Much has been made about the frayed relationship between the two groups — M.L.B., which is run by the owners of the 30 clubs, and the union, which is run by the players — that led to the sport’s first work stoppage in 26 years. And the heads of the two sides rarely meet face to face: Manfred, a labor lawyer who rose to the commissioner’s office in 2015, and Tony Clark, a former player who was tabbed as the union leader in 2013.

The two have disagreed on many matters. But they have also made deals, such as the 2016 collective bargaining agreement that has come to be viewed as having tipped the scales further in the owners’ favor.

The years since have taken a harsher tone. Players became increasingly vocal about the problems they saw in the game, from the lack of competition among some teams to the players’ lagging share of the game’s revenue to how they felt like mere pieces in a chess game run by front offices. Once complacent, many players became more active in their union. And for this very fight against owners, who ran an $11 billion-a-year industry before the pandemic, the union brought in a new lead negotiator.

So after a 99-day lockout instituted by M.L.B., after much jockeying, after more frustration festered, after lulls and deadlocks in talks, after repeated attempts to create pressure by issuing threats or deadlines, a new labor pact was reached in time to fit in a full 162-game regular season.

The interests of management and workers don’t always align, and tension is thus inherent in labor relations. But believing he needed to do a better job in improving the tenor of the relationship between the sides, Manfred called Clark with a message on Thursday afternoon.

“I told him that I thought we had a great opportunity for the game in front of us and told him that I hope to work with him on things that are new in the agreement, like the effort to get to the international draft or more generally on seizing the opportunity that is in front of us,” Manfred said Thursday night at M.L.B.’s headquarters in Manhattan.

At a news conference the following day at the union offices a few blocks away, Clark explained that Manfred had called to congratulate him on approving the new five-year C.B.A.

“I responded accordingly and suggested to him that there’s a lot of work to do moving forward with respect to where our game is at and where it needs to head,” Clark said. “I look forward to having those conversations.”

The implementation of an international draft, as Manfred noted, is one of those conversations. After it presented a roadblock in talks earlier in the week, the sides found a solution: Table it for now. They set a July 25 deadline for deciding on the draft. If it is accepted, the players get their end of the trade: the elimination of the qualifying offer, a draft-pick compensation system that hinders a handful of players’ free agency each winter. If the draft is not approved, the status quo remains on both matters.

Another of the steps in which Manfred said he hoped things could improve with the players: the more regular collaboration the sides will have starting in 2023 on a joint committee majority controlled by M.L.B. that will consider rule changes and implement them after 45 days’ notice. This way the sides can together try to improve a game that has been dominated by strikeouts, home runs and walks, a contrast to Manfred’s previous ability to do so unilaterally after giving one year’s notice or with union consent.

While players were not initially fond of the notion of surrendering some of that control, they ultimately agreed to do so because it came with trade-offs for other improvements they sought. That’s the nature of bargaining, and the players did this elsewhere, too.

After arguing that the luxury tax thresholds had not grown in past deals at the same rate as club revenues, players wanted them higher, and they eventually got that. Although the annual growth in the threshold during the period covered by the deal is 3 percent, the increase from the lowest threshold — starting at $210 million in 2021, to $230 million in 2022 — is the largest they have had from one agreement to the next. To get that, the players agreed to a new, fourth threshold at $60 million over the base — with very stiff penalties — that may limit the select few biggest-spending teams (the Los Angeles Dodgers and the Mets).

As in any negotiation, particularly where significant change is sought, the lists of initial demands are high. Until recently, for example, owners had been seeking luxury tax penalties that were more than double the previous agreement. Until January, the union had been seeking ways for players to reach both free agency and salary arbitration sooner.

“It’s difficult, but we’re never going to give up on some of those things,” said Bruce Meyer, the lead union negotiator. “This is the labor process. We have determined adversaries on the other side, all of whom are billionaires, and they have enormous resources. Our players did an incredible job of sticking together. And ultimately we’re comfortable with the deal that we have. Whether more can be accomplished in the future, we’ll have to see.”

Where players had some of their most notable advancements was in how young players will be compensated. The jump from a minimum salary of $570,500 in 2022 to $700,000 in 2023 is the biggest single-year increase in major league history. A $50 million bonus pool will be created for top young players who are not yet eligible for raises under salary arbitration.

In a phone interview, Gerrit Cole, a star Yankees pitcher and a top union leader, also pointed to other gains: a lottery for the top six spots in the domestic amateur draft so “if an owner is hellbent on tanking, that’s his prerogative, but it’s going to be a lot harder to do that.” Cole also said the union had gained the right to give a full year of service time to players who finish in the top two in Rookie of the Year Award voting, avoiding another Kris Bryant situation.

Manfred called this labor deal “an olive branch” in terms of building a better relationship with players. He also said the moves favoring players in this agreement, such as in the luxury tax system, would “probably” lead to “a little different market results.”

Asked if the measures players had sought would be enough to address their original concerns, Clark said that he was hopeful but that time would tell over the next five years. Meyer noted that there had been instances in which players had pushed for more in certain areas, such as how to address tanking, but that owners had resisted.

“Some of the changes that we’ve put in a new C.B.A. will be felt over time,” he added. “Some of these things aren’t going to kick in overnight. Things like the draft lottery, promoting competition and other ones are not necessarily going to be seen yet.”