"It was on my mind, but you couldn't think about it too much," Headley said. "To go out and compete against a guy like Ryan Braun, I was a little nervous, but everything turned out great.
"It's just neat. It's a tremendous honor."
Headley doubled home a run in the fifth inning, moments after his drive down the right-field line was called a home run but reversed when the umpires looked at a video replay.
Headley hit an RBI triple in the seventh and scored the go-ahead run on a sacrifice fly by Yonder Alonso.
Headley also drew two walks and finished with a .286 batting average. His previous RBIs high was 64 in 2009.
"For Chase to hang on to the RBI lead was a great thing," San Diego manager Bud Black said. "It was awesome. That RBI thing was real. Our guys felt it. And looking over at their side, I think they felt it, too. They were sensing what was going on."
San Diego improved by five wins this year and wound up with a 76-86 record. The Padres won only five of their last 15 games.
Travis Ishikawa drove in four runs for Milwaukee, including three with a double in the third that made it 6-0. The Brewers went 83-79, a drop of 13 wins after reaching the NL championship series last year.
Since Aug. 20, Milwaukee's 29-13 record was tops in the majors. The Brewers got within 1 1/2 games of St. Louis in the chase for the second wild-card berth, but that was dashed with a 3-6 stretch in late September.
"It's always disappointing when you don't make it to the playoffs when you figure you have a team that is championship caliber," Milwaukee manager Ron Roenicke said."The whole season? A disappointment.
"But when I look back at where we were and where we ended up, I'm really happy with where we went."
Cameron Maybin hit a two-run homer for San Diego, and five relievers held Milwaukee hitless in the final six innings.
"It was a good win, and our bullpen was tremendous," Black said.
Braun went 1-for-4. He led the NL with 41 homers and 108 runs, and ranked first in extra-base hits, slugging percentage and total bases. Braun was second in RBIs with 112 and third in batting at .319.
Braun won the NL MVP last year when he hit .332 with 33 homers, 111 RBIs and 109 runs. He faced a 50-game suspension after testing positive for elevated testosterone, but the players' union appealed and the test result was overturned by baseball arbitrator Shyam Das.
"I think ultimately we'll look back on the season as a positive," Braun said. "At the beginning of the year, if you would have told us we'd miss out on the postseason, I think we'd all be disappointed. But at the same time, you have to reassess your goals when you consider everything we've dealt with as a team.
"Injuries, trades, new guys coming up, 12 games under .500. To finish over .500 is definitely an accomplishment. Getting back into the race, playing meaningful games in September up until the last three games is something we're really proud of. Hopefully we can build on this heading into next year."
San Diego SS Everth Cabrera finished with 44 stolen bases to become the first Padres player to lead the league in that category. ... 3B Aramis Ramirez, who joined Milwaukee in the offseason, was taken out before the start of the third inning. He went out for warm-ups and received a nice hand when he was replaced by Jeff Bianchi. Ramirez set a team record for most RBIs by a third baseman (103) when he drove in a run in the first. ... The Brewers are the first team to lead the NL in home runs and stolen bases since the 1996 Rockies.