The game was tied 3-3 after three innings and neither team was able to push across a run for the next 15 1/2 innings.
Lugo walked with one out in the 19th and took third on a single by Jordan Schafer. Scott Procter followed with a ground ball to Pittsburgh third baseman Pedro Alvarez, who threw home. Catcher Michael McKenry caught the ball about 3 feet up the line and made a sweeping attempt to tag Lugo.
McKenry appeared to have made contact and turned to home plate Jerry Meals for confirmation while Lugo's first reaction seemed to be that he thought he was out. But Meals signaled safe, ending the game and setting off a lengthy argument. Video of the play seemed to support all initial reactions except Meals'.
"I saw the tag but he looked like he (missed) him and I called him safe for that," Meals said. "I looked at the replays and it appears he might have got him on the shin area. I'm guessing he might have got him but when I was out there when it happened I didn't see a tag.
"I just saw the glove sweep up. I didn't see the glove hit his leg."
Major League Baseball released a statement Wednesday acknowledging Meals had blown the call.
"Unfortunately, it appears that the call was missed, as Jerry Meals acknowledged after the game," MLB Executive Vice President for Baseball Operations Joe Torre said. "Many swipe tags are not applied to the runner with solid contact, but the tag was applied and the game should have remained tied.
"I have spoken with Jerry, who is a hard-working, respected umpire, and no one feels worse than him. We know that this is not a product of a lack of effort."
That call ended a 6-hour, 39-minute game that was the longest in either teams' history. They combined to use 41 players.
Scott Procter (2-3), the eighth Atlanta pitcher in the game, picked up the win after he pitched three innings of one-hit relief. Daniel McCutchen (3-2) got the loss after giving up three hits and four walks -- and the 19th-inning run -- over 5 1/3 innings.
Pittsburgh scored its three runs in the first two innings. Neil Walker tripled in one run and scored another in the first inning and McKenry hit a home run in the second for the other. It was his second home run of the year.
Atlanta scored three times in the third, with Jason Heyward's two-run single capping the rally.