Striker Nelson Kangunje tapped in the winner on the 82nd minute to end Wanderers dream of a double after they earlier lifted Carlsberg Cup.
Victory marked a remarkable turnaround in the fortunes for Civo, who barely four months ago, were in TNM Super League relegation zone after going eight games without a win, piling pressure on coach Oscar Kaunda.
However, the youthful Kaunda had the last laugh as he earned Civo their first title since 2009, and were $18,323 richer in addition to the trophy in the annual competition sponsored by Standard Bank Malawi.
It was Civo’s first win having twice lost in the final in 2009 and 2010 when Kaunda was an assistant coach.
It was the first time this decade that Wanderers have lost in the final in six attempts.
Wanderers defeated Blue Eagles 1-0 in the semifinal whereas Civo stunned Big Bullets 2-1 a fortnight ago to qualify for the final.