The Braves, already assured a playoff berth, won their fourth in a row.
Maholm (13-10) won for only the second time in his last seven starts by blanking the Marlins on five hits over 6 2/3 innings.
Craig Kimbrel worked the ninth and made his 40th save an unusual one by striking out four batters in the inning. The second of his victims, Donovan Solano, reached first base when the third strike got past catcher Brian McCann for what was ruled a wild pitch.
Kimbrel then went on to strike out John Buck and Gil Velazquez to end the game.
Martin Prado drove in two of Atlanta's runs with a solo homer in the first and a single in the third.
The loss went to Josh Johnson (8-14), who allowed three runs on four hits with five walks in six innings. It was Miami's sixth straight setback.