The Swiss bowed out of the event in the French capital at the quarter-final stage after a 7-6 (7-5) 7-5 defeat, with the Canadian bolstering his hopes of reaching the ATP World Tour Finals in London.
However, it serves as a major blow for Federer and his attempts to end the year atop the rankings for a sixth time.
Victory for world number one Novak Djokovic in Paris could put him 1,310 points clear of Federer in second going into the end-of-season showpiece, but the 17-time grand slam winner insists he will prepare well to keep his dream alive.
"I always thought it was going to get solved in London," he told the ATP's official website.
"What this [loss] means is I will have a good preparation for London. It's not that I didn't want to win here, but I knew it was going to be tough from the start. I accept that. Now I will continue to prepare for London.
"I'm going to stay on indoors now. Obviously two days more is big. So I'm looking forward to some days off right now, really resting my body to the max in a short period of time.
"I have plenty of days now to get ready for London, which is kind of nice, as well. So I can actually properly practise for a change as well again."