NEW YORK -- Technically, the Padres won their third-inning challenge on Tuesday night. It certainly didn't feel that way.

San Diego fell victim to a controversial replay ruling, which put an abrupt halt to a third-inning rally in their 6-3 loss to the Mets at Citi Field. Then, the Padres had a protest attempt nullified by the review process as well.

On the play in question, a run was awarded, but the Padres saw their inning end because Carlos Asuaje had been thrown out at third base -- after the third out had already been called.

"I think they completely misapplied that rule," Padres manager Andy Green would say afterward.

Confused? Let's start at the beginning.

San Diego loaded the bases with two outs against Mets starter Zack Wheeler in the third. William Myers blooped a single into left field, scoring one run before Manuel Margot was called out on a close play at the plate.

Once Margot was ruled out, Mets catcher Devin Mesoraco threw to third base, where a jogging Asuaje was tagged by Phillip Evans . Third-base umpire Laz Diaz ruled Asuaje out, even though the inning was believed to be over anyway.

"As soon as I saw him call the third out, I started slowing down," Asuaje said. "I handed [third-base coach Glenn Hoffman] my helmet and I just didn't think anything of it."

"It was just kind of a reaction," Mesoraco said of his throw to third base. "I wasn't 100 percent aware of the rule of how it plays out. I wasn't sure, and I wasn't sure that I got [Margot] out. It didn't hurt anything to throw down to third and get that tag, so it worked out. … You just never know. You can't assume anything."

The Padres challenged the play at the plate, and replays confirmed that Margot's slide had beaten Mesoraco's tag. Diaz pointed to the plate and signaled that Margot was indeed safe. The Mets lead became 3-2.

A moment later, Diaz gestured to third base and ruled Asuaje out, sparking the controversy.

"I don't know how you think he's making a full-bore effort to advance to third base," Green said. "I think it's a lethargic jog toward the third-base coach, which is pretty customary when the third out of an inning is made. You go hand the guy your helmet. That's effectively what was happening."

The replay official did not see it that way.

"The runner attempting to advance to third base was unaffected by the incorrect call and was tagged by the fielder," MLB's statement read.

Section IV of MLB's replay regulations covers the placement of runners after incorrect calls. Here is the segment in question:

Subsequent Calls and Outs: If the Replay Official determines that an incorrect call on the field had no effect on the subsequent behavior or conduct of the offensive or defensive players, the Replay Official shall change the incorrect call, but let stand any on-field calls or plays unaffected by the incorrect call. The Replay Official may not declare a runner out based on a play the umpire believes would have occurred subsequent to the play subject to Replay Review.

"We told everybody in Spring Training, in these instances now with replay, you have to play every ball out," said Mets skipper Mickey Callaway. "That was a heads-up play by [Mesoraco] to continue the play and get us a big out right there."

The Padres contended that the call at the plate had a drastic impact on Asuaje's actions. After the game, Asuaje wondered aloud what he should have done on the basepaths, given that the inning was already deemed over.

"I guess the safest thing would be to just stay at second and, if there's a close play or something, just wait on the base," Asuaje said. "I really don't know how else to do that. Nobody's going to play that ball through -- especially with the third baseman standing there. My only move would be to go full-speed and slide into the guy. What if that was the third out at home? What are we going to do? Are we going to fight these guys? I mean, I'm not going to start a brawl."

Shortly after Diaz issued the ruling, Green emerged to argue his case for Asuaje to be placed at second. He then asked to protest the interpretation of those rules, but according to section II.L.4. of the replay regulations, "No protest shall ever be permitted on judgement decisions by the replay official." He was denied.

The Mets won somewhat handily, but few would argue that the third inning served as the game's turning point. The Padres would have had two men on base for Eric Hosmer . Instead, New York scored two in the bottom of the frame on a Michael Conforto homer.

"Down one run, runners on first and second and one of our best hitters coming to the plate, we have the opportunity to tie or take the lead," Green said. "That does change trajectories of baseball games. But I'm not going to sit here and put that game on top of that call."

AJ Cassavell covers the Padres for MLB.com. Follow him on Twitter @ajcassavell.