The Group E result made sure the Ivorians would join Ghana and hosts South Africa in next year's tournament but the battle for three remaining berths from the region hung in the balance.
Cameroon stayed ahead in Group A after dispatching Togo 3-0 in Yaounde, while African champions Egypt kept alive their hopes with a 1-0 away win in Zambia.
With the Ivorians needing only a draw against bottom placed Malawi in their qualifier in Blantyre, coach Vahid Halilhodzic rested most of his key players for what was presumed a routine challenge.
But after Malawi broke the deadlock in the 63rd minute through Jacob Ngwira, Halilhodzic was forced to introduce the might of Drogba, who had been left on the bench along with Barcelona midfielder Yaya Toure.
The Ivorian captain took just two minutes from his entry on to the field to score the equaliser and secure a second successive World Cup trip for the west Africans.
MOVED LEVEL
Cameroon are one point ahead of Gabon in Group A while Egypt moved level with Algeria on 10 points in Group C.
Hosni Abd Rabou scored with a thunderous long-range effort in the 69th minute to give Egypt a 1-0 win in Chililabombwe.
Algeria are expected to restore their three-point lead when they host bottom-placed Rwanda in Blida on Sunday, setting up a potentially thrilling deciding match in Cairo between Egypt and Algeria next month.
Cameroon and Gabon are also set for an exciting finale in Group A after they both won their last home matches.
Cameroon's Geremi scored after missing a first half penalty while Jean Makoun and Achille Emana added second half goals in their rout of Togo.
Gabon ended Morocco's slim hopes with Hull City's Daniel Cousin among the goal scorers.
Cameron and Gabon will both play their last qualifiers away next month.
Six African qualifiers will be played on Sunday, including Group B leaders Tunisia against Kenya. Nigeria, who trail Tunisia by two points, will face Mozambique.
