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.