McInnes is using the early games of his reign to get a handle on what he has at his disposal and handed 17-year-old Craig Storie a debut in midfield, one of four changes from the side that had drawn at Hibernian on Monday night. Captain Russell Anderson missed out through injury.
Kilmarnock had lost 1-0 to Hearts in their previous match, and made three changes to the side which had started that game, but left the firepower of Kris Boyd and Cillian Sheridan on the bench.
Both sides were still feeling their way into the game when McGinn struck after just four minutes. Stephen Hughes angled a ball to McGinn wide on the left, and the former Celtic man slipped the ball through the legs of Ross Barbour before curling a fabulous strike high beyond Rangers-bound goalkeeper Cammy Bell.
After 25 minutes, the Dons should have had a second goal. Storie's pass to Jonny Hayes set up a quick breakaway, and the winger played a good low ball towards Scott Vernon at the near post, only for the former Oldham man to completely miss his kick.
McInnes shuffled his pack at the interval, with Gavin Rae replacing young Storie in the midfield, and the Dons started the second half brightly.
They had already forced a couple of corners when Joe Shaughnessy's forceful run into the box allowed McGinn another chance to shoot from 12 yards, but Bell saved well.
McInnes had spoken in the build-up to the match of the importance of providing entertainment, to tempt back the dwindling crowds - only 6,334 turned out for this one - in the Granite City, and McGinn was the only player showing that spark in this game.
With 20 minutes left, Boyd got his head to a cross from Barbour, but succeeded only in flicking the ball wide of the far post.
The Dons had suddenly sprung into life and Ryan Jack got in on the act, forcing a fine save from Bell before the ball fell to Josh Magennis who sent his shot into the ground, taking all the power out of the effort and leaving Bell to mop up comfortably.