Jason Heyward singled twice and scored two runs for the Braves while Luis Avilan (1-0) won on a day Atlanta used eight pitchers to hold Pittsburgh to four hits.
"We got some stuff accomplished today and we got the win," said Braves manager Fredi Gonzalez. "A lot of good stuff."
Burnett (16-10) gave up four runs in 5 2-3 innings for Pittsburgh. The Pirates finished 79-83, extending their record streak of losing seasons to 20.
"We needed to win our games," manager Clint Hurdle said. "Our goal was to win more games."
A regular-season finale that looked like it might be important a month ago had a decidedly spring training feel after the Pirates collapsed down the stretch.
Pittsburgh was 62-46 on Aug. 8 but finished on a 17-37 slide, though the team's 79 wins tied for the most since the infamous streak began following a loss to the Braves in the 1992 NL championship series.
"You have to try and take some positives from it," said McCutchen, who hit .327 this season to finish second behind San Francisco's Buster Posey for the NL batting title. "Every year is hard to take when you don't end up where you want to be. Every year is tough."
Maybe none, however, were more painful than this one. The Pirates were the talk of baseball over the summer behind a pitching staff that flourished behind Burnett, who embraced the roll of ace the team desperately needed. He won eight straight decisions in the spring but tailed off over the final two months and couldn't avoid his fifth loss in his six starts, though he exited to a warm ovation.
"I thought he had an exceptional season," Hurdle said of Burnett. "He took ownership of the trade, the career, the opportunity to re-ignite himself."
NOTES: The Pirates drew 2,091, 918 to PNC Park this season, the second-highest total in team history. The average attendance of 26,149 was up from 23,956 in 2011 ... The Braves will start RHP Kris Medlen (10-1, 1.57 ERA) Friday against Kyle Lohse (16-3, 2.86) ... The Pirates open the 2013 season at home on April 1 against the Chicago Cubs.