Senegal manager Ferdinand Coly said on Sunday that "Senegal will accept the sanctions". He also apologised to Ivory Coast.
Trouble flared after striker Didier Drogba scored his side's second goal from the penalty spot.
Visiting supporters were forced to leap down on to the pitch to escape as violence erupted, with home fans throwing missiles, stones, bottles and firecrackers.
Ivorian players took refuge in the centre circle while the security forces used tear gas to disperse the rioting fans.
The match was suspended for 40 minutes while police tried to restore order but the referee was forced to call off the second-leg, final-round qualifier.
Caf says its decision to ban Senegal is in accordance with the provisions of article 16 paragraph 20 of their regulations of the competition, which states: "If the referee is forced to stop the match before the end of the regular time because of invasion of the field or aggression against the visiting team, the host team shall be considered loser and shall be eliminated from the competition, without prejudice to the sanctions existing in the regulations."
Ivory Coast had already been included in Monday's seedings draw for the 2013 Nations Cup , which will be held in South Africa between 19 January and 10 February.