"Roger has been looking to make a change for some time," GWR chairman Ralph Bernard told the paper. "He was 50 a few weeks ago and the time had come to consider other options."
Darren Henley, the "light classical" station's managing editor since 2000, will replace Lewis.
Lewis is moving to Wales to become managing director of ITV Wales, a less prominent position than the one he held at Classic FM. The step down has fueled rumors that Lewis was in some way forced out of the company following the merger.
"There will always be conspiracy theorists," Bernard told the Guardian. Lewis has not made a public statement about his departure.
The merger between GWR and Capital Radio creates the UK's largest commercial radio group, with 55 local radio stations and 93 digital radio stations that reach an estimated 18 million listeners, the companies say.