Martino guided Atlanta to a 21-7-6 regular-season record, good for second place in the Eastern Conference and in the league overall.
The former Argentina and Barcelona manager has also led Atlanta through the Eastern Conference semifinal round, with a date against the league-best New York Red Bulls upcoming in the conference final.
Martino has helped Atlanta to an extremely successful start to life in MLS, with the club making the playoffs in both of its first two seasons in the league.
Along the way Martino has helped attract some top talent to MLS, with stars Miguel Almiron and Josef Martinez both named league MVP finalists this season.
The manager has imposed a relentless attacking style on his side, with Atlanta the first team in league history to post consecutive 70-goal seasons.
Martino's successful run in Atlanta is set to end, however, with the manager already having announced he will leave the club at the end of the season amid links to the vacant Mexico job.
Martino won the award with 32.72 percent of the overall total vote, which includes votes from players, club officials and the media.