The Ayrshire businessman had been co-opted into the club's board in 2010 so as to allow him to set up his 10000Hours project, which aimed to secure a 51% stake in the Paisley club.
A consortium of directors - led by chairman Stewart Gilmour - had expressed a wish to sell their shares but rejected an offer of £1.25m from 10000Hours in September as they doubted it would be sustainable. It is thought that some directors were concerned that Atkinson's presence on the board might put off other interested suitors.
"I wish the club well," said Atkinson in a statement last night. "And, in particular, I wish to thank the board, staff, team, management and, of course, the great fans for their support."