The Cameroonian international missed the weekend clash with Newcastle but will reclaim his place between the posts for this crucial European tie.
"He will play tomorrow," said Amorim, when asked about Onana.
The first leg in France ended 2-2, leaving everything to play for as United look to capitalise on home advantage and secure a spot in the semi-finals.
Altay Bayindir, who made his Premier League debut in Onana's absence, is expected to return to the bench.
United's preparations are hampered by a number of injuries. Joshua Zirkzee has been ruled out for the rest of the season after sustaining an injury against Newcastle.
"Joshua is out for the season," said Amorim. "So he's not going to play more this season. Let's prepare him for the next one.
"It's tough, especially in this moment. I think he's improving in all aspects of the game, so it's hard for any player to stop, but this is football and he has to be ready now to recover."
Lisandro Martinez remains a long-term absentee, while Ayden Heaven is also unavailable. Midfielder Toby Collyer continues to be sidelined, and Amad is still working individually as he builds match fitness.
Jonny Evans has resumed training but won't be in the squad for Thursday's clash.
There is some encouragement for United, with Matthijs de Ligt expected to feature again before the end of the season, though his involvement against Lyon is not yet confirmed.
Manchester United staged a breathtaking comeback at Old Trafford, overturning a two-goal extra-time deficit to defeat 10-man Lyon 5-4, securing a Europa League semi-final clash with Athletic Bilbao.
Ivory Coast legend Emmanuel Eboue has urged Manchester United winger Amad Diallo to focus on building physical strength if he wants to stay injury-free and reach elite levels in his career.
Manchester United head coach Ruben Amorim has admitted that his side are not currently ready to compete in the Champions League, both in terms of quality and structure.
Bruno Fernandes has revealed the most electric Old Trafford atmosphere he has experienced during his five years at Manchester United.
