The Peoples Team, who have never won the Standard Bank Cup, had hoped to bring down the curtain to reach the finals.
Chiukepo Msowoya gave Bullets the lead at Kamuzu Stadium through a header in the 18th minute of the first half, but in-form Raphael Phiri, formerly of Karonga United equalised in the second half before he snaffled another winner to silence the vocal Biafra stands.
It is close to 10 years since Civo United last reached a final, but victory was a just reward for a side which has been transformed since Oscar Kaunda succeeded Thom Mkorongo as coach.
Bullets, without a trophy since Mabvuto Lungu became coach, could have few complaints about the outcome.
Mid-way through the second half, both sides made changes that were to lead to the tempo of the game to change, especially Civo dominating each and every minute.
Big Bullets woes in this half was a result of reverting to a 3-4-3 formation after they pulled out Miracle Gabeya in defence for Doverson Mlozi to add fire power upfront.
However, it was Oscar Kaunda’s tactical switch brought nstant dividends, as his side terrorized Bullets defence, which lacked team leader and confidence.
With Bullets still readjusting to the new system of three defenders, Gerald Nkungula raided into space down Bullets left and cut the ball back for Nelson Kangunje who beat two defenders before his shot was saved by Chimwemwe Kunkwawa.
Bullets’ play was crying out for an attacking focal point and in the 70th minute their technical panel sent on Mlozi for Gabeya , which saw repositioning of players in another re-shuffle.
But it was Civo’s football bristled with attacking intent and in the 74th minute Yamikani Fodya cleared the ball on the line to the relief of their fans.
In the 76th minute Kangunje cantered down the left flank and back-heeled the ball to, Emmanuel Zoya apparently nerveless -old playmaker, who rolled a pass into the box for Chikondi Likwemba to clear inside the 18 yard box.
It should have been 3-1 in the 83rd minute, but when the ball rolled into Nkungula’s path after John Lanjesi had slid in to thwart Bullets defence, the agile defender miscued his shot.
There were wild celebrations after the last whistle, when Civo United players danced all the way to ganyu supporters, as they chanted, “ Ma Civil Servant, agona mtown ( Civil Servants have slept in town).
Civo will now expect to meet the winner between Blue Eagles and Mighty Be Forward Wanderers who lock horns on Saturday at Civo Stadium in Lilongwe.