Molina lined the first pitch from Scott Proctor to the top of the brick facade in right and the ball ricocheted back to the grass in right field.
Molina stayed at first and Emmanuel Burriss rushed out to pinch run, while Giants manager Bruce Bochy hustled out to argue. After a brief discussion, the umpiring crew headed to the replay booth in the umpires room behind home plate.
After about two minutes, they returned and crew chief Tim Welke signaled the home run. Dodgers manager Joe Torre then came out to discuss the situation.
After a total delay of about 15 minutes, the umpiring crew ruled Burriss had to stay in the game and he was credited for the run scored, prompting San Francisco to play the remainder of the game under protest.
This marked the seventh time this year that replay had been used and the second time Friday. The other call that was reversed was on Sept. 19, when Tampa Bay's Carlos Pena was awarded a home run that was originally ruled a double.
Replay was used for the first time at the Giants' waterfront ballpark. There also was replay used Friday in the Nationals-Phillies game at Philadelphia.
The system that allows umpires to determine boundary calls went into use on Aug. 28.
