The Australian international was dropped from the side which drew with Hamburg in the Europa League midweek but came on in the 67th minute to make an immediate impact, scoring twice with 12 minutes of being on the pitch to give Celtic a lead before it was cut back late in the game.
Mowbray admitted that there is currently some jockeying for positions at Parkhead but was happy to see McDonald get himself back to top form.
"There is competition for places," Mowbray said.
"I'm delighted that he scored a couple of goals. From my perspective you'd like to be in the position where you don't leave Scott on the bench because he scores every single week.
"But he has had a few weeks where he has had some chances and the keeper has made good saves but hopefully those goals will help his confidence."