The 27-year-old delayed his appearance for the tournament in the Ivory Coast due to his commitment to his club.
Talks were held between the English club and Onana's country to ensure his availability for Sunday's draw with Tottenham Hotspur – a game which ended 2-2.
Whilst fans moved out of Old Trafford after the game, Onana jetted off to begin the 4,800-mile journey from Manchester on a private jet to the Ivory Coast.
The former Ajax shot-stopper will, however, not be available for Cameroon's AFCON opener against Guinea on Monday 15 January.
The Indomitable Lions have been drawn in Group C of the tournament, alongside Senegal, Guinea and the Gambia.
Onana retired from international duty last year after disagreements with Cameroon coach Rigobert Song saw him sent home from the 2022 World Cup.
The goalkeeper later rescinded his decision and revealed his readiness to represent his country going forward.
Onana’s late arrival means he will not start his country’s first AFCON group game and it remains to be seen whether he’ll be in post in their second match.