Despite a four-match winless run, Malawi found form at the right time in Blantyre.
A double from Gabadin Mhango gave them their victory, with his first goal coming in the seventh minute.
And Mhango's second effort - which came 21 minutes from time – gives them a healthy advantage heading into next month's second leg.
Benin also won 2-0 with their success at Sao Tome E Principe greatly helping their cause.
Other results saw Ismael Diakite's second-half strike give Mauritania a 1-0 triumph against Equatorial Guinea.
And Namibia edged Congo by the same scoreline thanks to Rudolf Bester's 88th-minute goal.
Seychelles – originally scheduled to play Gambia – have a bye into the second round of qualifying.
Gambia were disqualified from all Confederation of African Football competitions for two years for deliberately playing overage players in last month's Under-20 championship.
