Amarista was initially called out, but Padres manager Bud Black challenged, and the call was overturned after a three-minute, 42-second review made it clear that Amarista had avoided Pena's tag with a clever twisting move.
Amarista scored later in the inning on a sacrifice fly by Everth Cabrera to put San Diego up 2-0.
Then, in the top of the eighth, Atlanta challenged a play involving Amarista's defense.
With a runner on, Freddie Freeman grounded to shortstop Cabrera to start a potential double play. But Amarista lost the ball while exchanging it from his glove to his hand, and second-base umpire Stu Scheurwater called Tommy La Stella safe at second.
Black challenged, and the call was overturned to send La Stella back to the Braves' dugout.
On the very next play, virtually the same play unfolded when Justin Upton grounded into a fielder's choice to short. Amarista dropped the ball on the exchange again, but Freeman was called out this time.
Atlanta manager Fredi Gonzalez challenged, but the call stood. The Braves didn't score any runs in the inning.
Will Laws is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.