Rennes' French defender #17 Guela Doue (left) fights for the ball with AC Milan's US midfielder #80 Yunus Musah during the UEFA Europa League round of 16 play-off match between Rennes and AC Milan at The Roazhon Park Stadium in Rennes, western France, on Feb 22, 2024. (PHOTO / AFP)

RENNES, France - AC Milan reached the Europa League last 16 despite a 3-2 loss at Stade Rennais on Thursday as Benjamin Bourigeaud's hat-trick was not enough for the hosts to stop the Italian side completing a 5-3 aggregate victory.

Azerbaijan's Qarabag advanced after a thrilling game against Portuguese side Braga which they lost 3-2 after extra time but won the tie 6-5 on aggregate.

Rennes, facing an uphill battle after Milan secured an emphatic 3-0 home win in the first leg, started aggressively in rainy conditions.

Bourigeaud scored with a shot into the bottom corner after 11 minutes before Luka Jovic levelled with a powerful header.

Bourigeaud converted a penalty nine minutes into the second half after Simon Kjaer's trip on Martin Terrier, before Rafael Leao equalized in the 58th minute for Milan.

Rennes' Adrien Truffert (right) kicks the ball by AC Milan's Christian Pulisic during the Europa League soccer match between Rennes and AC Milan at the Roazhon Park stadium in Rennes, western France, on Feb 22, 2024. (PHOTO / AP)

"We gave it our all from start to finish, regardless of the position we were in and the goals we conceded. This hat-trick is the reward for a whole team’s effort," Bourigeaud told UEFA.com.

Rennes were awarded another penalty in the 68th minute after a handball by Jovic and Bourigeaud completed his hat-trick from the spot.

ALSO READ: Depleted Milan miss chance to go second with 4-2 loss at Monza

"We will all have our opinions coming back, but we have qualified. Getting through to the next round seemed easy in the first leg, it wasn’t an easy affair, but we still have a lot of situations to evaluate," Milan manager Stefano Pioli told Sky Sports Italy.

Milan, who dropped into the Europa League after finishing third in their Champions League group, will find out who they play in the round of 16 on Friday.

"I think tonight’s match confirmed that we have a lot of potential going forwards. But we have to concede fewer chances against our opponents," Pioli added.

Garabagh's Azerbaijan midfielder #27 Toral Bayramov and Sporting Braga's Portuguese midfielder #11 Roger Fernandes vie for the ball during the UEFA Europa League Last 16 second leg football match between Qarabag FK and SC Braga in Baku on Feb 22, 2024. (PHOTO / AFP)

Qarabag, down to 10 men early in the second half, forced their match against Braga into extra time before Nariman Akhundzade's late goal sent them through.

Benfica and Toulouse shared the spoils in a goalless draw as the Portuguese champions advanced to the last 16 after beating the struggling French 2-1 team at home in the first leg.

Freiburg beat Lens 3-2 after extra time following a goalless first leg in France.

David Costa and Elye Wahi scored for Lens before the break and Roland Sallai pulled one back for hosts Freiburg before equalizing in stoppage time.

READ MORE: Milan miss two penalties, 10-man Juve stalled by Empoli

Michael Gregoritsch emerged as Freiburg's hero with a goal in extra time to send the German side into the last 16.