The two teams battled through 12 1/2 scoreless frames before Gindl, playing in his 13th big-league game, sliced a pitch from Ryan Webb (1-4) just over the fence in the left-field corner for the walkoff homer.
John Axford (4-3) earned the victory with a scoreless top of the 13th as five Brewers pitchers combined on a four-hit shutout.
Milwaukee starter Wily Peralta surrendered just two hits in eight scoreless innings, walking two and striking out seven.
Marlins counterpart Henderson Alvarez also pitched well, blanking the Brewers on five hits over seven innings. He walked one and struck out one.