The Stanley Okumbi coached outfit went to the encounter from an 11-match unbeaten run but they failed to show the form against the hosts.
Gibrilla Wobay and Umaru Bangura scored for Sierra Leone before China-based striker Michael Olunga pulled one back for Kenya.
The John Keister coached side started the match on a high note forcing Kenyans to run behind for the first 14th minutes.
The hosts got their first free-kick on the 3rd minute and piled more pressure on Harambee Stars thereafter; a situation which saw Ayub Timbe go to the referee’s book twice and Brian Mandela shown the red card. Timbe was yellow-carded in the 7th minute for a foul and added another one at the stroke of half-time for altercation.
Julius Wobay put Sierra Leone ahead in the 22th minute after flipping past defenders to beat Boniface Oluoch in goal. The goal served as a wakeup call for Kenya and Captain Victor Wanyama almost leveled matters two minutes later with a header which missed the target by a whisker.
In the 37th minute, Victor Wanyama’s shot was deflected by Sierra Leone keeper Zombo Morris then Michael Olunga met the rebound but the strike hit the bar to give the hosts time for clearing the danger.
By this time, you could feel the tension inside the pitch. Kenya were under immense pressure and as a result, they suffered a bow in the 40th minute.
Defender Brian Mandela was sent off for dangerously sliding on striker Alhassan Kamara inside the box, leaving Harambee Stars one man down.
Head coach Stanley Okumbi introduced David ‘Cheche’ Ochieng’ and Samuel Onyango in the second-half in a bid to bring the game back to life.
However, it was Lione Stars, who continued shining brighter, doubling the lead in the 68th minute from the spot courtesy of Umaru Bangura.
Kenya then registered a consolation four minutes later through Michael Olunga, who drilled in a beauty from free-kick.
And that’s how Kenya nose-dived to the bottom position of Group F behind Ghana and Ethiopia who will play their first round match on Sunday.
Sierra Leone Starting XI: Zombo Morris, Hassan Milla Sesay, Umaru Bangura, David Simbo, Yeami Dunia, Medo Kamara, Alfred Sankoh, Kwamie Quee, Gibrilla Wobay, Kei Kamara and Alhassan Kamara.
Subs: Alhaji Dauda Conteh, Ibrahim Bangura, John Kamara, Khalifa Jabbie, Abdul Sesay, Michael Lahoud, Mohamed Buya Turay.
Kenya Starting XI: Boniface Oluoch (GK), Musa Mohammed, Eric Ouma, David Owino, Brian Mandela, Victor Wanyama, Anthony Akumu, Eric Johanna, Ayub Timbe, Masoud Juma, Michael Olunga.
Subs: Patrick Matasi, Simon Mbugua, Joseph Okumu, David Ochieng, Samuel Onyango, Stephen Waruru, Ernest Wendo.