After Marte blasted a triple off the wall in right field off Tim Hudson, Hunter Pence gathered the ball and relayed to second baseman Ehire Adrianza, whose throw to third got away from Pablo Sandoval.
Marte took off for home and slid head-first, extending his right arm as the tag was applied by Buster Posey. Home plate umpire Quinn Wolcott called Marte out, but Pirates manager Clint Hurdle challenged the play.
After a review, the umpires determined Marte's right arm touched home plate before the tag.
Marte went 2-for-4 and scored both Pittsburgh runs as the Pirates edged the San Francisco Giants 2-1 on Tuesday to take the middle test of this three- game set.
Charlie Morton allowed just an unearned run on three hits over eight dominant innings for the Pirates, with Tony Watson (3-0) tossing a scoreless top of the ninth to earn the win.
Hudson (4-2) was charged with one earned run on five hits with five strikeouts over 8 2/3 innings.