The Phillies will open the best-of-five division series at home Wednesday against Colorado. Cole Hamels or Cliff Lee likely will get the Game 1 start.
Hanley Ramirez got the day off and finished with a .342 average to become the first Marlins player to win a batting title. He also is the first NL shortstop to win the batting title since Dick Groat in 1960.
Marlins left fielder Chris Coghlan had three hits to bolster his bid for NL Rookie of the Year. His 113 hits after the All-Star break tied with Juan Pierre (2004) and Bill Buckner (1980) for the most in the last 45 years.
Ryan Howard, Jimmy Rollins and Chase Utley were among the resting Phillies starters. Just one RBI shy of 100, right fielder Jayson Werth started and went 1 for 4, missing out on the milestone. The crowd erupted in jeers when Werth was intentionally walked with two outs and the winning run on second in the 10th inning.
Howard led the NL with 141 RBIs and was second in homers with 45. Center fielder Shane Victorino led the league with 13 triples.
A sellout crowd of 45,211 packed Citizens Bank Park for the finale. That brought Philadelphia's final attendance totals to 73 sellouts and a record 3,600,693 fans.
Miguel Cairo homered for the NL East champions, who finished 45-36 at home. Chad Durbin (2-2) got the win with one inning of scoreless relief.
The Marlins went 87-75 under third-year manager Fredi Gonzalez. While Gonzalez was widely praised for keeping the Marlins in wild-card contention until the final weeks with the lowest payroll in baseball, he was forced to respond to a story saying the team may replace him.
ESPN.com reported former Mets manager Bobby Valentine, who recently ended a six-year run as manager of the Chiba Lotte Marines in Japan's Pacific League, is in talks about taking a position with the Marlins.
"As we looked at the performance at things that happened, games that went one way, games that went another way, there is no question we felt we should have been a playoff team," Marlins president David Samson said.
Dan Meyer (3-2) took the loss for the Marlins, who finished with a winning record for only the sixth time in franchise history.
The Phillies (93-69) will open the postseason at home for the third consecutive year. They lost in the division series to Colorado in 2007 and kicked off their run to the championship last season by eliminating Milwaukee.
It's the Rockies again standing in their way.
"Last year, we thought, 'OK we were there last year,"' Victorino said. "Now, we just have to go out and play. That's what it's going to be like this year. We're the world champs."
NOTES: Phillies CF Ben Francisco was caught stealing three times. He was nailed at third for the second out in the ninth inning. ... Werth's 20th stolen base gave the Phillies three members of the 20-20 club, along with Rollins and Utley.