The Edinburgh, Scotland, native, 2007 IndyCar Series champion and Indianapolis 500 winner, was in his rookie season on the Sprint Cup season.
His No. 40 Dodge was 41st in points without a top-10 finish in 10 starts on the Sprint circuit, with his best finish 22nd-place at Goody's Cool Orange 500 at Martinsville, Va., in March.
"This is a difficult decision for (co-owner) Felix (Sabates) and I that did not come without its share of anguish," Ganassi said in a release Tuesday. "In this tough business environment, continuing to run the car without proper funding has become increasingly difficult."
Ganassi has two other cars which will still compete in Sprint Cup racing -- the No. 41 Dodge driven by Reed Sorenson and the No. 42 Dodge driven by Juan Pablo Montoya.
Ganassi hopes Franchitti will continue to drive in the Nationwide Series.