The 23-year-old made the move to Old Trafford in 2018 but failed to make a single first-team appearance during this time with the 20-time English champions.
Kovar spent time out on loan with Swindon Town and Burton Albion before starring with Sparta Prague during the 2022-23 campaign, featuring on 32 occasions for the Czech outfit in all competitions.
The goalkeeper was involved in Man United's preparations for the 2023-24 campaign, and there had been claims that he could be a part of the goalkeeping set-up at Old Trafford this term.
However, it has now been confirmed that Leverkusen have signed him on a deal until June 2027, with the deal allegedly costing an initial €5m (£4.3m), which could rise to €8m (£6.9m) with add-ons.
Leverkusen sporting director Simon Rolfes told the club's official website: "Matej Kovar is big, strong in one-on-ones and is very good with his feet. He's a player with great prospects and we have high hopes for him in the coming years."
Meanwhile, Kovar added: "I'm very excited about the quality of this team. From what I've seen so far, I can hardly wait for the next few years."
While confirming the move, Man United said in a statement: "Manchester United Academy graduate Matej Kovar has joined Bayer Leverkusen in a permanent transfer, subject to international clearance.
"Everyone at Manchester United would like to thank Matej for his service to the club and to wish him all the best for the future."
Tom Heaton's calf injury during a training session last week led to Dean Henderson being named on the bench as back-up to Andre Onana against Wolverhampton Wanderers on Monday night.
Henderson continues to be linked with a switch to Nottingham Forest, but Heaton's injury could allegedly see the England international remain at the club as second choice to Onana, at least until the January transfer window.