Thiago Almada's free kick sailed into the back of the net, largely thanks to an error from Onana, as Lyon took the lead on home soil, but Leny Yoro's header in the final stages of the first period levelled the scores.
The 20-time English champions were the better outfit in the second period and received their reward in the 88th minute when Joshua Zirkzee headed an excellent Bruno Fernandes cross into the back of the net from close range.
However, that was not the end of the drama, with Rayan Cherki levelling for Lyon in the fifth minute of added time at the end of the 90 when Onana palmed a straightforward strike from Georges Mikautadze into a dangerous area, levelling the tie delicately poised ahead of the return fixture at Old Trafford next week.
SPORTS MOLE'S VERDICT
Whisper it quietly, but Man United are suddenly looking like a team, and that statement remains true despite the Red Devils conceding a second late on, with a famous victory being taken away from them.
This was a strong night for Man United, with the English side putting in a statement performance in Europe to leave themselves in a solid spot when it comes to reaching the semi-finals of the tournament, but it should have been better.
It has been a season to forget in the Premier League, but Man United are the favourites for the Europa League for a reason, and make no mistake, Ruben Amorim's side deserved to claim a victory for their troubles.
Yoro was sensational in the middle of the defence, while Fernandes again ran the show from the middle of the park, and Man United will always have a chance of winning matches while the Portugal international is in the side.
It was almost perfect aside from two big mistakes from Onana, and Man United need to enter the transfer market for a new goalkeeper this summer, as the Cameroonian has too often come up short in the biggest of moments.
LYON VS. MAN UNITED HIGHLIGHTS
Thiago Almada goal vs. Man United (25th min, Lyon 1-0 Man United)
Lyon take the lead in the 25th minute, and it is a horror moment from Onana, as the Man United goalkeeper allows a free kick from Almada to end up in the back of the net; it is a huge error from the Cameroonian.
Leny Yoro goal vs. Lyon (45th min, Lyon 1-1 Man United)
Man United level the scores in the final moments of the first half, and the goal comes from Yoro, who converts an effort from Manuel Ugarte into the corner of the net; it is an instinctive header from the centre-back, as he registers his first Man United goal.
Joshua Zirkzee goal vs. Lyon (88th min, Lyon 1-2 Man United)
Huge moment in this match, as Zirkzee heads a cross from Fernandes into the back of the net to send Man United 2-1 ahead. Has the Netherlands international just won the first leg for the Red Devils?
Rayan Cherki goal vs. Lyon (95th min, Lyon 2-2 Man United)
Lyon level the scores in the fifth minute of added time at the end of the 90, as Cherki fires into the back of the net from close range after Onana had palmed a shot from Mikautadze into a dangerous area.
MAN OF THE MATCH - LENY YORO
Fernandes was again sensational for Man United, with the captain leading the charge, but he was just overshadowed by Yoro, with the teenager putting in a wonderful performance in the middle of the away team's defence.
Yoro levelled the scores late in the first period with an excellent header, but it was his overall display that impressed the most, with the Frenchman carrying the ball forward for his side, and this was comfortably his best outing for the club.
LYON VS. MAN UNITED MATCH STATS
Possession: Lyon 54%-46% Man United
Shots: Lyon 16-13 Man United
Shots on target: Lyon 5-5 Man United
Corners: Lyon 5-8 Man United
Fouls: Lyon 10-14 Man United
BEST STATS
WHAT NEXT?
Man United's attention will now switch back to the Premier League, preparing to tackle Newcastle United in the competition on Sunday afternoon; Amorim's team are 13th in the Premier League table.
Lyon, meanwhile, will be back in Ligue 1 action on Sunday evening against Auxerre; Paulo Fonseca's side are currently fifth in the Ligue 1 table, two points behind third-placed Monaco.
Written by
Matt Law