Kenya got off to a better start with the rejigged forward line of Edwin Lavatsa and Rama Salim forcing the Malawian rearguard to desperately scramble away balls in their box.
Stars bossed possession, 52 percent of it until close to the end of the half when Bernard Mangoli and Jockins Atudo fell injured.
Coach James Nandwa was forced to withdraw Mangoli and bring AFC Leopards forward in the 41st minute dealing a blow to his pre-match plans.
Malawi came alive at this point with their midfield lynchpin James Kamwendo firing just wide from range as the Stars re-organisation opened up the centre of the pack.
The recovered Atudo had the last chance of the half when he fired his free kick straight to Malawi keeper Charles Swini when Salim was brought down at the edge of the box.
Kenya had four shots against three on target with the match set to go to penalties if the game stays locked at 0-0
Stars have not beaten Malawi in their last eight outings and in June, Kinnah Phiri’s charges frustrated an entire nation when they held Stars to a barren draw in their opening World Cup qualifier in a match Malawi could have gone ahead and won.
Waiting for either side in the semi are Zanzibar, who prevailed on post match penalties against Burundi, who face Kenya’s other team in a African Home Nations Championship (CHAN) qualifier on Saturday in Nairobi.
This is the first time in three editions that Kenya, the five-time winners of the regional trophy, have wriggled out of the group stages of the tournament.
STARS FIRST XI- Duncan Ochieng, Anthony Kimani (C), Jockins Atudo, David Owino, Abdallah Juma, David Ochieng, Bernard Mangoli (Mike Baraza), Humphrey Mieno, Clifton Miheso, Rama Salim, Edwin Lavatsa.
FLAMES FIRST XI- Charles Swini, Steve Changoma, Moses Chavula (C), Foster Namwera, John Lanjesi, Ndaziona Chatsalira, Miciam Mhone, Joseph Kamwendo, Chimango Kayira, Rodrick Gonani, Chiukwepo Msowoya