Holmes netted for just the second time this season when he curled in from 20 yards before the 25-year-old crossed for the impressive Will Hayhurst to add a second.
Jack King wasted a fine chance to add a third goal in the second half as Simon Grayson earned a win in his first home game as Preston manager.
North End were ahead after six minutes. Holmes collected a throw-in before ghosting inside to curl a stunner past goalkeeper Steve Arnold.
And the Lilywhites doubled their lead in the 16th minute. Holmes turned provider as his deep cross was guided home by Hayhurst.
Preston could have extended their lead early in the second half but King fired over from six yards out.
Stevenage rang the changes after the hour and improved, with Robin Shroot firing over from inside the box before fellow substitute Steve Beleck headed wide.
Hayhurst stung the palms of Arnold and Lucas Akins forced Declan Rudd to save in the dying minutes but neither side could score again as struggling Stevenage were condemned to a fifth consecutive away defeat.