Sam Ssimbwa side were in desperate need of a win after they lost their opening 3-0 to Bandari at home last weekend.
But Elli Asieche scored the all-important goal in the stoppage time to hand Ssimbwa his first win of the season.
Batoto Ba Mungu made their intention clear early in the game with a push for a goal to try and destabilize their opponents. Kelvin Kimani came close to breaking the deadlock but was denied by the custodian.
Alan Wanga raced clear into Sofapaka danger area, but the visitors repelled that attack with a watertight defence. Homeboyz were giving as much as they received and it took Mathias Kigonya's intervention in the 30th minute to deny Wycliffe Opondo from close range.
Sssimbwa threw in Stephen Waruru and Asieche who had come in for former KCB man Teddy Osok, in the second half, and it was the latter who beat the offside trap to bury Hillary Echesa's inch-perfect pass.
Elsewhere, Nakumatt came from two goals down to draw 3-3 with Thika United.
Clement Mata gave Nicholas Muyoti side a deserved lead in the seventh minute after defensive lapses. Saad Musa made it 2-0 a few minutes later before Cornelius Juma halved the scores.
Mata completed his brace in the 44th minute after a good move that caught the opponents flat-footed.
With a few minutes to half time, Thika conceded a penalty and defender Donald Mosoti made it 2-3 before Brian Nyakan came in with an equalizing goal.
Chemelil Sugar and Bandari FC played to a barren draw at Mbaraki Stadium, Mombasa.