Mwafulirwa, who has been scoring regularly for the Urban Warriors, opened the scoring in the 30th minute with a simple tap in after being set through by former Jomo Cosmos striker Esau Kanyenda.
Provider turned scorer on the dot of half time when the Russia-based Kanyenda dribbled his way past three markers to score the second for the Flames.
Substitute Noel Mkandawire, who was brought in after Kanyenda was sent off for a second bookable offence, added the third goal with a long range shot deep in the second half to seal the victory.
The result gave some relief to Flames coach Stephen Constantine who is under fire to resign after going six games without a win.
Commenting on the game, Mwafulirwa told Kick Off that he was happy that the Flames had finally won.
“We had to fight for the pride of our nation and I hope we will build on this result in future,” the Ajax man added.
Malawi featured four other South Africa based players, Peter Mponda, Robert Ng’ambi of Black Leopards, Santos’ Tawonga Chimodzi (second half substitute) and Dynamos’ goalkeeper Swadick Sanudi.