The Northern Irishman was in last place following the first round at Dundonald in Ayrshire after three closing double bogeys saw him card an eight-over 80.
Clarke pulled out of the Scottish event on Friday morning but indicated that his withdrawal was precautionary.
The 2011 Open champion, 48, hasn't made a cut on the European Tour this year.
2016 European Ryder Cup captain Clarke, now ranked 1016 in the world, has missed 13 successive cuts since last year's Open and has not had a top-10 finish on the European Tour since his 2011 major triumph at Royal St George's.
Clarke plans to continue his career on the seniors tour when he turns 50 in August of next year.
Past champion Darren Clarke expects to play in The Open at Royal Birkdale next week despite pulling out of the Scottish Open because of a knee injury.