The former Barcelona and Argentina manager received an average of 32.7 percent of the votes from players, media and front offices around the league to edge Los Angeles FC's Bob Bradley (22.3) and Sporting Kansas City's Peter Vermes (10.9 percent).
Atlanta finished behind the New York Red Bulls to earn the second of six Eastern Conference playoff berths and have since reached the penultimate round of the postseason.
They will face the top seeded New York Red Bulls in a two-legged conference championship in late November.
Under Martino, who successfully mixed star players alongside developing young talents, Atlanta outscored every MLS club with 70 goals, posted the best regular season road record (10-5-2) and tied the previous all-time points record with 69.
Martino, who was United's first coach, has led the club to consecutive postseason appearances with a fast-paced attack and by securing the most aggregate points from the last two MLS campaigns, Atlanta earned a berth in next year's CONCACAF Champions League.
Martino, however, will not lead them into that competition, as he has already decided not to exercise the option on his contract to stay beyond this season. (Reporting by Frank Pingue in Toronto Editing by Toby Davis)
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