The Arsenal manager felt that Sokratis Papastathopoulos' red card proved his side's undoing in a 3-1 loss to the Ligue 1 side on Thursday.
Arsenal were unable to control the first leg of their Europa League last-16 tie with Rennes as they wanted after Sokratis Papastathopoulos' red card, according to Unai Emery.
The Gunners took a third-minute lead through Alex Iwobi but Sokratis received two yellow cards in the space of seven minutes and Benjamin Bourigeaud equalised with a thunderous strike before half-time.
An own goal from Nacho Monreal was followed by Ismaila Sarr heading home at the end of a swift break two minutes before the final whistle, sealing a surprise 3-1 victory for the Ligue 1 side.
Emery – a three-time winner of the Europa League with Sevilla – felt Arsenal controlled the match until Sokratis' dismissal and paid the price for failing to stifle a late Rennes break.
"We controlled the first 40 minutes of the game. After the red card we could not control it," Emery told BT Sport.
"We wanted to hold the positioning with one player less, but also take chances to transition or to get possession around the box. We had one chance with Mesut [Özil] but it's [not] enough.
"When it was 2-1, thinking it's difficult to have a better result, we wanted to hold it but, the transition is another bad action for us and they won.
"They won the first 90 minutes, but we have another 90 minutes at home with our supporters and we want to think positive now. It will be 11 against 11 and when we were playing 11 against 11 the team was playing well."
Sarr's strike came nine minutes after Emery sacrificed Pierre-Emerick Aubameyang in a bid to shore things up defensively.
Emery said: "I decided not to give Eddie Nketiah the big responsibility of these matches, but it's one transition and we lost this situation.
"When we had one less player on the pitch I think we could've done better, but we didn't control and didn't [perform in a way to] hold the result. It can be different [in the second leg], but we need to be more compact."