Nady, who hit two homers in the Pirates' extra-innings win in the series opener, drove in Nyjer Morgan with a 10th-inning single and the Pirates beat the Braves 4-3 on Thursday night.
The Braves used seven pitchers after Hampton's much-anticipated comeback was postponed because he injured a chest muscle in pregame warm-ups.
The bad news: the injury will send him back to the disabled list.
"Nobody's more disappointed than I am," Hampton said. "As hard as it was for me to say, I had to tell them I couldn't go."
Hampton was only minutes away from making his first start since Aug. 19, 2005, when he hurt himself after making what manager Bobby Cox called 23 "excellent" warm-up pitches.
"It's unbelievable something else could pop up like that but it did," Cox said.
Hampton will be placed on the 15-day disabled list, retroactive to Saturday, and left-hander Jo-Jo Reyes will be called up from Triple-A Richmond on Friday.
"I feel deep in my heart that it's going to be a short-term thing," Hampton said.
The umpires were already on the field before word came out that Hampton was hurt. The start of the game was pushed back seven minutes and fill-in starter Jeff Bennett was allowed time to warm up.
Cox plans to activate Chuck James from the disabled list to take Hampton's spot in the rotation. Reyes will pitch out of the bullpen which could use the help; the Braves used seven pitchers Thursday night, seven on Wednesday, and nine in the first game of the series on Monday.
Hampton's absence forced the Braves to get creative with their bullpen. Chris Resop started the 10th on the mound, moved to left field for a batter to set up a lefty-on-lefty matchup, and then went back to the mound. Once there, Resop (0-1) gave up Nady's go-ahead single.
Les Lancaster was the last major leaguer to pitch, play in the field and go back to the mound in the same inning, according to the Elias Sports Bureau. He did it for the Chicago Cubs on June 13, 1990, in the first game of a doubleheader against the New York Mets.
The Pirates also have a new injury concern, after shortstop Jack Wilson left the game after straining his left calf while running out a tying single in the seventh inning.
Wilson likely will miss Friday's game at Florida but said he doesn't think his injury is serious.
"When I wake up tomorrow I hope it will be good to go," Wilson said before adding it's "not likely" he will play Friday.
"It's one of those muscles that will heal pretty soon. ... It was not a sharp pain."
The Pirates won Monday in the first game of the series 12-11 in 12 innings.
Resop walked Morgan to lead off the 10th. Morgan moved to second on a sacrifice bunt by Luis Rivas. Resop also walked Jason Bay, and Corky Miller couldn't handle ball four, allowing Morgan to move to third.
"With [Atlanta's] lineup, you don't know if one run or five will be enough," Nady said. "It was nice to win the series."
Tyler Yates (1-0) earned the win by pitching a scoreless ninth inning.
Bennett gave up four hits and two runs in four innings.
Zach Duke shut out the Braves for five innings but gave up three runs on three hits and a fielding error by Wilson in the sixth.
2B Freddy Sanchez, who was limited by a sore right shoulder in spring training, left in the sixth inning. Manager John Russell said Sanchez was taken out of the game "just as a precaution." ... Bennett has appeared in three of the Braves' four games.