"It didn't feel too good when we got back," Jones said. "The off-day definitely helped. It felt a lot better this morning."
Jones, who had arthroscopic surgery in Spring Training, had his knee swell on a trip from Houston to Atlanta after he came off the disabled list and had to have it drained, missing the Braves' first two home games against the Brewers.
The third baseman then played just the middle two games of a four-game set in Arizona and sat out the opener with the Dodgers before celebrating his 40th birthday on Tuesday with a home run and having a big hit on Wednesday.
Going into the series against the Pirates, the Braves were 9-2 when Jones played, and 3-5 when he didn't.
"We want to keep him fresh and productive all season," Braves manager Fredi Gonzalez said. "Sometime this weekend, we'll give him a breather."
Jones, who finished the road trip batting .278 with three homers and 10 RBIs, hit sixth again on Friday night, with Freddie Freeman third, Brian McCann fourth and Dan Uggla fifth. In his 10 starts, Jones has batted third three times, fourth once and sixth five times.
The Braves have used 15 different lineups in 20 games, but have stuck with the same one for the past three games.