The Gunners, who went off around Evens (2.0) at Roazhon Park, looked to be on their way to the quarter finals when Alex Iwobi put them ahead in the early stages.
The tie turned on its head just before half-time though. Sokratis Papastathopoulos picked up two bookings in seven minutes and was given his marching orders by referee Ivan Kruzliak.
Rennes struck back immediately against the 10 men and went on to claim a 3-1 win, utilising the additional space out wide with Hatem Ben Arfa looking a constant threat.
Ismaila Sarr's strike in the dying minutes added gloss to what was an accomplished second half performance and leaves the Premier League team with plenty to do next week.
bet365 now make Rennes a 4/6 (1.67) chance to qualify for the next round with Arsenal priced at 11/10 (2.10) to progress at the Emirates. With further participation in serious doubt Unai Emery’s side have drifted to 8/1 (9.0) in the outright betting.
In terms of the second leg in isolation, the Gunners have been a popular selection at 3/10 (1.30) to win in 90 minutes but they will need to do so by two clear goals to have a chance of being in the draw for the quarter finals.
Chelsea had no such problems and cemented their position at the top of the market with a 3-0 win over Dynamo Kiev. Maurizio Sarri’s side are now 11/4 (3.75) ahead of Napoli (10/3) who also took a commanding first leg advantage from their clash with Red Bull Salzburg.