United have confirmed that the centre-back has been ruled out of their final two games in the Premier League, against Huddersfield and Cardiff.
The Ivorian international has started just 13 games all season for United and has only completed 90 minutes twice since January, as a series of issues blighted his spring.
Bailly's 2018/19 is now over, having played fewer than 1000 minutes in a miserable campaign that comes off the back of a 2017/18 season where he only started 13 games.
United are expected to invest heavily in defence this summer, with Kalidou Koulibaly and Milian Skriniar among the centre-backs that have caught their eye.
The Old Trafford club will also buy a right-back this summer, with Aaron Wan-Bissaka and Kieran Trippier both boasting advocates among the United hierarchy.
Bailly signed from Villarreal in the summer of 2016 for a fee of around £30 million and impressed during his debut season before struggling for fitness in the next two campaigns. He was helped off in the second half of United's 1-1 draw with Chelsea at Old Trafford on Sunday.
The African Cup of Nations takes place June 21-July 19 in Egypt this summer.
The Ivorians are in a group with South Africa, Morocco and Namibia in the 24-team tournament.
Additional reporting by agencies
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