Ryan Howard was thrown out by a wide margin at home plate in the sixth inning, but the call was overturned after replay because it was ruled catcher Miguel Montero blocked Howard's lane to the plate.
Howard's run proved to be the difference as the Phillies beat the D-backs, 4-2, to take two of three games of this series at Citizens Bank Park.
With two outs in the sixth, D-backs starter Vidal Nuno walked Howard and Marlon Byrd followed with a towering popup to shallow right-center.
Second baseman Didi Gregorius backpedaled, settled under the ball and then backpedaled some more and the ball hit off his glove.
"When it went up, I was underneath it and the wind took it further than I thought," Gregorius said. "And [right fielder Gerardo] Parra didn't see it either, so I decided to call it and it hit my glove and it dropped. So it's my mistake."
Howard, who didn't appear to be running hard, was out easily at the plate, but upon replay review it was determined that Montero violated rule 7.13, which was instituted this year to prevent collisions at home plate.
Regardless of the rule, it could have been avoided had Gregorius made the catch or if Parra had seen it and called him off.
Howard's run gave the Phillies a 3-2 lead and poor defense cost the D-backs one inning later when left fielder David Peralta clanked a fly ball with two outs, allowing Wil Nieves to score.
So while they may not have been happy about the replay call, the D-backs were in no way using it as an excuse for the loss.
"We had a chance to win that game, and the rule didn't cost us that game," D-backs manager Kirk Gibson said. "We should have caught the ball."
And what about the one that Peralta missed in left?
"I think you expect to make that play," Gibson said. "But we didn't. We had an opportunity to win the game, but we didn't play good enough on the other side of the ball, as well."
All of the defensive follies overshadowed a quality outing by Nuno, who deserved a better fate.
"It's not frustrating," Nuno said. "It's just part of the game. We battled the whole game. The team needed a strong outing and for me to go deep in the ballgame, so [I] just made pitches and defense came through at times, but those sun balls were kind of tough right there. It's just part of the game sometimes."
The left-hander allowed two earned runs over 6 2/3 innings while throwing a career-high 117 pitches.
"He threw the ball very well," Gibson said. "Pitched good enough to get the win."
Not that Nuno was blameless in the outcome. He had Howard down 0-2 before issuing the walk to him in the sixth.
"Two-out walks were really his only flaw," Gibson said of Nuno's outing.
The two earned runs came in the first inning when Nuno walked Chase Utley with two outs and then allowed a home run to Howard.
"I was just looking for something to try to drive," Howard said. "It was a fastball. It looked like it was little bit down, and I got something to drive and it carried a little bit farther than I thought it was, and I'm happy that it did."
The D-backs managed to tie the game off Phillies starter Roberto Hernandez thanks to an RBI double by Nick Ahmed in the second and a sac fly by Paul Goldschmidt in the sixth.