Helms told The Miami Herald last week that he felt comfortable in his utility role with the Marlins and had informed the team of his desire to return.
Helms, who was typically used as a pinch-hitter, spot starter, or late-inning defensive replacement at one of the corner infield spots, hit .243 with five home runs. As a pinch-hitter, Helms went 13 for 41 (.317) with two home runs. The Marlins obtained Helms earlier in the season from the Phillies.
Terms of the contract were unknown. Helms' old contract with the Phillies contained a $750,000 buyout for 2009, which the Marlins inherited when they obtained him in April.
Helms, 32, has also played with the Brewers and Braves in his 10 major-league seasons.
His pinch-hit home run on Sunday at Shea Stadium snapped a 2-2 tie and helped to propel the Marlins to a 4-2 victory that eliminated the Mets from the playoffs.
It was only five years ago when Ugueth Urbina was the king of the hill for the Marlins as their top reliever. He was on the the mound for the 2003 Marlins when they clinched the wild card, defeated the San Francisco Giants in the deciding game of the NLDS, and knocked off the Chicago Cubs in Game 7 of the NLCS.
The acquisition of Urbina ranks as one of the most significant mid-season trades in the history of the Marlins, who gave up Adrian Gonzalez to land him on July 11, 2003. Urbina appeared in 33 regular season games for the Marlins and 10 in the postseason.
The Marlins continued tweaking their 40-man roster, outrighting outfielder Alejandro De Aza and relievers Henry Owens, Lee Gardner and Doug Waechter to Triple A New Orleans. That leaves the Marlins with 38 players on the 40-man.
De Aza (ankle) and Owens (shoulder) spent the entire season on the disabled list while Gardner (right elbow) was on the DL from mid-April on.
In another transaction, minor-league pitcher Scott Nestor was claimed off waivers by the Phillies.
-- The Marlins announced on Wednesday that Ryan Tucker and Logan Morrison were the organization's Minor League Pitcher and Player of the Year, respectively.
Tucker, a right-hander, went 5-3 with 1.58 ERA in 25 appearances with the Double A Carolina Mudcats while Morrison hit .332 for Single A Jupiter.