Arsenal took an early lead through Alex Iwobi to give the visitors the perfect start with a precious away goal but the game then turned on a decision as Sokratis Papastathopoulos received a second yellow card and the Gunners were reduced to ten.
Rennes took advantage of their extra man in the second half and took the game to Arsenal and were rewarded as Nacho Monreal deflected a cross into his own net before Ismalia Sarr added a third for the French side late in the game.
Story of the match
Going in as strong favourites against the team who sit in 10th place in Ligue 1, the side from north London gave themselves the ideal start as Iwobi put them into an early lead.
With just four minutes gone Iwobi tried to find Pierre-Emerick Aubameyang at the back post but his misdirected cross curled into the back of the net off the post.
Arsenal then had the chance to double their lead as Iwobi seared forward into the box and pulled the ball back to Lucas Torreira, but his first-time effort was saved well by Tomas Koubek.
The away side looked to be in control of the match until Sokratis was dismissed after receiving a second yellow card as he cynically fouled Sarr as he broke behind the Arsenal defence.
Rennes immediately took advantage as Benjamin Bourigeaud fired a rocket into the top corner after his initial free-kick rebounded off the wall and fell kindly for him to strike.
Arsenal were then put to the sword in the second half and were put under big pressure by the home side and under the encouragement of a noisy home crowd they were rewarded as an unfortunate Monreal deflected Sarr’s cross into the back of his own net.
The French side continued to strive for a third goal to give them a good lead going into the second leg and Arsenal again cracked under the pressure of the relentless Rennes attack. Monreal was caught too high up the pitch which allowed Sarr to meet James Lea Siliki’s cross at the back post and direct a strong diving header past Petr Cech.
Uphill second leg task for Arsenal
Arsenal’s Europa League hopes now hang by a thread after a late third Rennes goal could prove to be extremely damaging to the Gunners.
With both Alexandre Lacazette and Sokratis suspended for the second leg, Arsenal will be without two likely starters in the return leg next Thursday at the Emirates Stadium.
The Gunners did overturn a one-goal deficit in the last round of the competition against BATE Borisov to win 3-0 in the second leg, however, up against tougher opposition in Stade Rennais, who proved their threat in attacking areas, Arsenal will face a difficult challenge.
The away goal scored in the early minutes of the match may prove to be vital for Arsenal as they need to defeat their French opposition by at least a two-goal cushion with 2-0 being enough to take them through to the next round.
With the places for a top-four finish in the Premier League looking increasingly competitive, next weeks second leg could prove to be a vital game for the Gunners season with a Europa League triumph offering a Champions League place.