Nigeria entered the tournament aiming for an 11th continental crown and a place at the World Cup in Brazil.
Abiodun, named in Justine Madugu's 25-player squad, was expected to be a key figure in the midfield.
However, Nigeria failed to qualify for the 2027 FIFA World Cup after losing 2-1 to South Africa in a playoff.
Abiodun ruled out of the season
Following her return to the Washington Spirit after participating in the WAFCON competition, the NWSL club confirmed on Monday that Abiodun will undergo surgery this week.
The 22-year-old was initially placed on the 45-day injury list earlier this month but has now been moved to the season-ending injury list, bringing her club campaign to a premature close.
Before her injury, Abiodun had made nine appearances for the Spirit, including four starts, accumulating 320 minutes on the pitch.
This professional setback comes as a big blow for the Super Falcons and their upcoming fixtures of games.
With her NWSL season now over, Abiodun faces a lengthy recovery period after a challenging few weeks for both club and country.
The midfielder will now focus on rehabilitation with the goal of returning to full strength for future campaigns.