Jacob Ngwira gave the Flames a 64th-minute lead in their African Zone, Group E qualifier, prompting visiting coach Vahid Halilhodžić to throw on the Chelsea striker.
Drogba's vindicated that substitution almost immediately, and his 67th-minute goal earned the Ivorians the point they needed to seal qualification.
The result took Côte d'Ivoire on to 13 points, an unassailable seven points clear of second-placed Burkina Faso, who play their penultimate game away to Guinea tomorrow.
Malawi moved on to four points - one above the Guineans - with the pool's top three finishers qualifying for next year's CAF African Cup of Nations in Angola.
Côte d'Ivoire, who are positioned first in Africa and 20th overall on the FIFA/Coca-Cola World Ranking, finished third in a very tough Group C at Germany 2006. After respective 2-1 losses to Argentina and the Netherlands, they beat Serbia and Montenegro 3-2 in an entertaining match.