Pittsburgh manager Clint Hurdle requested the review, feeling that the fan who ended up with the ball had reached over the wall for it.
Replays confirmed the original call and indicated the ball actually struck the fan in the midsection before he had touched it.
Morse's solo home run, his first in AT&T Park since May 15, cut the Pirates' lead to 3-1.
Tom Singer is a reporter for MLB.com and writes an MLBlog Change for a Nickel. He can also be found on Twitter @Tom_Singer. This story was not subject to the approval of Major League Baseball or its clubs.