Both teams started on high note but it was the Flames, participating as a guest team, who took the lead in the 15th minute through Chiukepo Msowoya who beat the Sudanese Keeper with a brilliant diving header.
The Desert Hawks however leveled matters five minutes later through Atahir El-Tahir with a thunderous shot.
In the second half, Flames coach Ernest Mtwali introduced Nelson Kangunje for Schumacher Kuwali in a bid to bring on fresh legs as Malawi opted for the counter.
But it was Sudan all over with several attacks in the second half in their quest for the equalizer.
Sudan were rewarded with a penalty on 85 minutes, but El-Tahir’s shot was saved by Malawi keeper Simplex Nthala as the Flames held on to claim a vital victory.
“We came to win this one as our first game and then take it from there in our second game because it’s a tricky group” said Mtwali.
In the other games of the day in the same group, Group C, South Sudan beat Djibouti 2-0.
Africa’s newest nation took the lead in the 28th minute through danger-man Bruno Martinez who tapped home from close range.
Dominic Abuyo sealed victory with a clinical finish on 72 minutes with a clinical finish.
“It’s a great win for us. Our target is the quarter finals and with this result we can make it” said South Sudan coach Lee Sung-Jea.
The win moves South Sudan to the summit of the group.