Coach Sebastien Migne was forced into making changes in the starting line-up, bringing in youngster Joseph Okumu in the central defense in place of Joash Onyango, who picked up a toe injury in training on Saturday.
Ayub Timbe was also given a chance on the right wing, with Johanna Omollo dropping out, as Eric Johanna took the creative role while Francis Kahata moved to the left wing.
Riyad Mahrez, an English Premier League winner with both Leicester City and Manchester City, was definitely not going to miss out from the Desert Foxes starting XI, nor was Baghdad Bounedjah, who manged three goals during the qualifiers.
It was the North African side who started the match on a high note, and they came close twice in the space of three minutes, but Baghdad failed to find the target, with Kenya custodian Patrick Matasi reacting fastest to put the ball out for a corner and deny Mohamed Belaili.
Aboud Omar lost possession in the Stars defensive area, and the Algerians almost capitalised on that, only for the latter to recover and commit a foul at the edge of the danger zone, but the resulting free-kick hit the wall and went out for corner.
Matasi was forced into a fine save in the 24th minute, stopping Belali's goal-bound effort after the Kenyan defense and midfield was caught napping.
Algeria continued pushing the East African side into making mistakes, and the pressure got the better of them eventually. The defenders resorted to clearing the balls from the danger zone without aiming them at specific targets.
After half an hour, the hosts got a deserved opener. The23-year old Youcef Atal danced his way into the 18-yard area, and was brought down by Dennis Odhiambo. The referee pointed to the penalty spot and striker Baghdad rose for the occasion, sending Matasi the wrong way.
It was the first penalty that the custodian had failed to save after stopping his previous three spot kicks while with the national team.
Algeria were superior in every aspect and dominated from the defense to attack.
With about 75% ball possession, a second goal was surely coming, and it happened in the 43rd minute. Ismael Bennacer lost his marker, pushed the ball to the byline before cutting the ball back to the unmarked Mahrez.
The Manchester City's forward's first-time shot took a deflection off Omar's on its way to the back of the net to give the Desert Foxes a healthy two-goal lead at the end of the first half.
Kenya looked more composed after the break, limiting the Algerians on the ball and shutting spaces quickly, but still they struggled to get the balls to isolated Michael Olunga in attack.
Attacks from the Harambee Stars were more evident with about 20 minutes to go, although their only meaningful chance fell to Olunga in the 74th minute, but the lanky striker's effort was blocked by the defenders.
Ayub Timbe managed to get into the danger zone in the 83rd minute, but his pass to Olunga was cut short by Atal, who sent the ball out for an unfruitful corner.
Kenya XI: 18. Patrick Matasi, 20. Philemon Otieno, 3. Abud Omar, 2. Joseph Okumu, 5. Musa Mohamed, 21. Dennis Odhiambo, 12. Victor Wanyama, 11. Francis Kahata, 7. Ayub Timbe, 10. Eric Johanna, 14. Michael Olunga.
Subs: 1. Faruk Shikalo, 23. John Oyemba, 13. Eric Ouma, 15. David Owino, 6. Bernard Ochieng, 17. Ismael Gonzalez, 19. Ovella Ochieng, 8. Johanna Omollo, 16. Paul Were, 9. John Avire, 22. Masud Juma.