Making only his third start since he moved from Derry City in January, McGinn was instrumental in dragging the visitors back from the loss of three goals in the first 19 minutes.
Mowbray later praised the 22-year-old and claimed he should have been utilised more by his team-mates, but as it was his direct style of play had the Austrian side on the back foot for much of the game.
The Irishman set up Marc-Antoine Fortune for his second goal but failed to cap a fine performance with a goal of his own, being denied on several occasions by Rapid keeper Raimund Hedl.
McGinn, who will shrug off a dead leg to travel to Gorgie, said: "It was my first start in Europe and I was disappointed not to get a goal.
"I scored against Kilmarnock in the league a few weeks ago so I am keen to get another and hopefully that will be against Hearts, if I'm picked of course.
"Hopefully I can keep my place in the team but even if I'm on the bench, I'm confident I can come on and make an impact.
"I didn't see much of the ball until we were 3-0 down against Rapid but after that I saw plenty of it, my confidence was high but I thought I should have scored.
"I was enjoying myself and I was annoyed that I had to come off.
"I went up for a header and their player put his knee into my leg. I wanted to play on but simply couldn't and hopefully I will be okay for Hearts after treatment.
"But any chance I get I want to make the most of it."
McGinn believes Celtic must shadow rivals Rangers all the way to their January meeting at Parkhead.
The race for the Scottish Premier League title race between the Glasgow giants continues apace.
After Sunday's trip to Hearts, Celtic play Hamilton at home on Boxing Day and then a trip to Kilmarnock in the following midweek comes before the Old Firm derby sees in 2010.
McGinn said: "It is important that we go in to the Old Firm game still winning games.
"We have hit form at the right time, we are playing well and we are scoring goals.
"Samaras and McDonald have been scoring goals and now Marc-Antoine Fortune is scoring and so the confidence is high.
"We won four games in a row before the draw against Rapid so we just need to keep the run of form going."
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