McGinn fired high into the net after just four minutes and though the Dons were rarely troubled by Kilmarnock, they were also unable to put the game to bed despite a number of chances - especially after the introduction of Josh Magennis midway through the second half.
McInnes said "I thought we were worthy winners. Jamie Langfield hasn't had a save to make the whole game but we made it more difficult than it had to be at times.
"We started with a real tempo and a bit of aggression about us. We couldn't have asked for a better start with Niall's finish. You can see why he's been so important to us.
"A real piece of quality won us the game, but we were wasteful and it should have been put to bed long before the 90 minutes were up.
"Kilmarnock, as they do, had plenty of possession of the ball and forced us to put an extra body in the middle of the park. But where we're falling short at the moment is putting the ball in the back of the net."
As McInnes evaluates his squad and tries to identify where the focus lies for next season, he handed a debut to 17-year old midfielder Craig Storie and though the youngster went off at the interval, the boss felt it was a useful exercise.
"We want to try and use a few younger ones and we will do that before the end of the season," he added. "Craig has been different class for us, and we've enjoyed working with him. He's shown a level of performance in the reserve team that justified him getting a sniff.
"That 45 minutes will be more beneficial than six months of reserve football. I thought he handled himself well and I have no doubt he'll go on to be a good player for Aberdeen."