Although Malawi were in a comfortable spot as far as qualifying for the next stage was concerned, they looked for a third successive win in Group B.
With key striker Frank Mhango benched for this particular encounter, the Flames netted through Chawanangwa Kaonga in the 31st minute.
However, their dominance would not yield the desired result in the second half as they wasted their chances in front of goal.
The Mambas of Mozambique would find the back of the net through Jeituso Mussica in injury time to seal a 1-1 draw, but that was not enough for them as they exited the competition.
In the other match that also got underway at 17:30, Namibia faced Seychelles and cruised past the Islanders via a 3-0 scoreline at Princess Magogo Stadium.
The Brave Warriors were fresh from a defeat against the Malawians and had to close their account with a victory.
With Namibia dominant in the early stages of the tie, they eventually found the back of the net in the 18th minute courtesy of Isaskar Gurirab.
Gurirab would then claim his brace in the 25th minute to ensure his country remained in the driving seat, thus adding to the opposition's woes.
Namibia killed off the encounter 65 minutes into the match when Sadney Urikhob made it 3-0 for the South West Africans.
Meanwhile, Malawi will now meet Chipolopolo of Zambia on Sunday, June 02 at the Princess Magogo Stadium.