The Gunners now have an uphill task on their hands to reach the quarter-finals , with the return leg at Emirates Stadium set to be played next Thursday.
Alex Iwobi gave Arsenal the lead in the tie after just three minutes, but after a fantastic Benjamin Bourigeaud strike levelled the scores, Nacho Monreal put the ball in his own net just after the hour mark.
Ismaila Sarr then ensured that Rennes claimed a significant win with a late goal , as Emery's men struggled to cope with the home side's energy and movement in the final third.
Ben Arfa played under the Spanish boss for a brief period at PSG, forced into a bit-part role from the sidelines after falling down the pecking order in his squad.
The 32-year-old was reduced to a role in the reserves before a bitter legal dispute saw him restored to the senior team, then ultimately ending up leaving the club to join Rennes last September.
“My motivation was to play a solid match, to win and get ourselves into a good position to go through," Ben Arfa began. "That’s what was in my head.
"But I did see the same Emery, as agitated as ever. I looked over at him a few times and that made me laugh a little. He hasn’t changed.
“I told some friends before the match that my prediction was that we would win 3-1 or 4-1. We didn’t manage to get the fourth but my prediction was right.”
Arsenal must now dust themselves down quickly ahead of a huge Premier League clash against Manchester United on Sunday.
Both teams are chasing the final Champions League spot in the league table, but the Gunners will have to produce a much-improved display to topple Ole Gunnar Solskjaer's rejuvenated Red Devils .
Meanwhile, Rennes and Ben Arfa will turn their attention back to Ligue 1 this weekend, with a vital home game against Caen to take in.