The Marlins were trailing 3-1 in the sixth when Hanley Ramirez (3-for-3) led off with a single off Jordan Zimmerman (3-5) and Stanton then pulled a 3-1 pitch over the left-field fence to tie the contest.
Logan Morrison followed with a double, went to third on Bryan Petersen's single came home with the go-ahead run on Chris Coghlan's sacrifice fly as the Marlins took the opener of a three-game home series.
Zambrano (3-3) earned the victory, yielding three runs on seven hits over six innings. The right-hander walked two and struck out five.
Zimmerman lasted six innings, allowing four runs on eight hits while socking a solo homer for the National League East-leading Nationals.