Clifton Miheso’s late goal saved coach Stanley Okumbi from an embarrassing defeat since he took over the team following the exit of Belgian Paul Put.
Wanyama put Kenya ahead from the penalty spot in the fourth minute, but Comoros leveled things up just two minutes later through Ajaccio’s midfielder and former Olympique Marseille youth graduate Youssuf M'Changama.
Kenya dominated the match with the Stars pitching camp on Comoros half, but they failed to take advantage of their possession to kill the game early enough with the two sides heading to the break tied at one-all.
The Islanders came back a more rejuvenated side in the second half, with dangerous runs along the left channel that gave Ismael Gonzalez and David Ochieng’ difficult time to deal with.
Kenya survived another scare from a free-kick delivered by Djamel Baker. But Comoros’ constant throbbing finally paid off when Amir Abdou charges doubled the lead in the 73rd minute from a Baker’s right footed close range shot that rested on the bottom corner with Patrick Matasi well beaten.
Matasi was forced to come out of his line for a timely save to keep Comoros at bay after the opponents broke Stars’ defence from the right flank as the Islanders pushed for another goal.
Girona striker, Michael Olunga was denied by the goalkeeper from a tight angle but Miheso made amends with an 83rd minute equalizer after he received a long ball, beat two defenders before firing a left foot shot into the net.
The match featured two teams that were looking for a big win. Kenya went into the tie with a record of three wins, two draws, in their last five games under former coach Paul Put while Comoros, before today boasted of two wins, two loses, and a draw in their last five games.
Comoros’ last game was a draw against Madagascar while Harambee Stars beat Zanzibar in the final to lift 2017 Cecafa Senior Challenge Cup last December.
Kenya will next take on the Central African Republic on Tuesday.
Kenya XI: Patrick Matasi (GK), Ismael Gonzalez, Abud Omar, David Owino, David Ochieng, Victor Wanyama (C), Johanna Omollo, Eric Johanna, Francis Kahata, Jesse Were and Michael Olunga.
Subs: John Oyemba (GK), Farouk Shikhalo (GK), Harun Shakava, Anthony Akumu, MacDonald Mariga, Samuel Onyango, Eric Kapaito, Clifton Miheso, Dancun Otieno, Patillah Omotto and Paul Were.