Ivory Coast were leading 2-0 on the night and 6-2 on aggregate - a result which seems likely to stand, sending Senegal out - when the match was stopped in the 72nd minute at the Stade Leopold Senghor.
Play had been temporarily halted in the 65th minute when a person ran on to the pitch and almost reached Ivory Coast striker Didier Drogba before being wrestled to the ground and escorted off the field.
Drogba had given his side the lead in the 51st minute with a free-kick and the former Chelsea man then made it 2-0 from the penalty spot in the 70th minute.
Following that second goal there were disturbances in the stands, with small fires being set alight and objects thrown as players and staff from both teams grouped together in the centre circle.
A host of Premier League players were involved in the match, including Newcastle pair Demba Ba and Papiss Cisse lining up for Senegal, along with West Ham's Mohamed Diame.
In Ivory Coast's starting line-up were Arsenal striker Gervinho, Manchester City brothers Yaya and Kolo Toure, and Newcastle midfielder Cheick Tiote.