A month after his San Diego Padres were knocked out of the playoff chase on the final day, Black nudged Cincinnati's Dusty Baker by one point for the NL award Wednesday.
"I guess this vote was sort of like our season, it came down to the wire," Black said on a conference call.
Gardenhire was the clear choice in the American League, earning the honor after five times as the runner-up. He led Minnesota to its sixth AL Central title in nine seasons.
"Congrats to the best manager in bestball!" Twins center fielder Denard Span tweeted. "Way overdue!" Span tweeted an apology moments later for misspelling baseball.
Said Gardenhire: "It's pretty neat to have your name mentioned up there."
Black was selected after guiding San Diego to a 15-game turnaround despite the second-lowest payroll in the majors. The Padres finished 90-72 and led the NL West until a late, 10-game slump and then a loss to San Francisco on the last day eliminated them.
"This was a great year in the NL," said Black. "I guess this vote could've gone either way. I feel fortunate that I won. All these guys are so deserving."
Baker, a three-time Manager of the Year, led the NL Central champion Reds to their first playoff spot since 1995. He was listed on 27 of the 32 ballots while Black was picked on 26.
"I'm not terribly disappointed because I didn't expect it," Baker told The Associated Press. "Buddy did a great job."
The announcement came on the one-year anniversary of Baker's father's death.
"When I woke up today, I was thinking about my dad, not the award," Baker said. "He'd be proud of me."
Two Baseball Writers Association of America voters from every league city send in three top choices when the regular season ends. Votes were counted on a 5-3-1 basis.