Malawi surprisingly grabbed the lead via Jacob Ngwira's goal four minutes past the hour mark.
Chelsea striker Didier Drogba, who came on as a second-half substitute, leveled the score four minutes later.
Ivory Coast's 100% record came to an end but they ensured they would finish the qualifiers on top of Group E to reach the World Cup for the second successive time, having made their debut in 2006.
Ghana have already qualified from Group D while South Africa will appear at the World Cup as the tournament hosts.
The race in Group A will go down to the wire after Cameroon and Gabon defeated Togo and Morocco respectively.
Three goals from Geremi Njitap, Jean Makoun and Achille Emana gave Cameroon a 3-0 victory over Togo, who will not be able to make a second successive appearance at the most important FIFA tournament.
Gabon claimed a 3-1 win over Morocco to become second in the group with nine points, one behind leaders Cameroon.
Cameroon face Morocco away from home while Togo host Gabon in their last games next month. Only the group winners reach the World Cup.