Kenya went into the second leg of their second-qualifying-round clash trailing 1-0, and with their preparations having been disrupted by a one-year suspension against Amrouche.
The Algerian tactician is alleged to have spat at an official during a qualifier against Comoros in May - with the Football Kenya Federation (FKF) appealing the resulting sanction to African football's governing body, the CAF.
In Amrouche's absence, James Nandwa led the national side for their vital clash in Nairobi, but he was unable to inspire a victory as they were held by a team ranked 29 places below them in the world to lose the tie on aggregate.
After what the FKF described as a "disastrous elimination", the body added in a statement that it "informs the public of its decision to sack the senior men's national team technical bench led by head coach Adel Amrouche".
"Losing the contest to Lesotho in the manner we did is unacceptable," the organisation added.
"The federation, with the support of the government, did everything to have the team ready for this match, including full settlement of allowances and even held our nerves to rally the Kenyan football fraternity to get behind Amrouche following his suspension by CAF.
"They have let the country down and as such they can have no further role to play in the affairs of the national team with immediate effect."
Elsewhere on Sunday, Mozambique joined Lesotho in moving into the group stages of qualifying as they saw off Tanzania 2-1 in the second leg to progress 4-3 on aggregate.
Joao Chissano's men move into Group F alongside Zambia, Cape Verde and Niger while Robert Ssentongo's late strike helped ease Uganda to a second-leg victory over Mauritania.
Leading 2-0 from their first leg in Kampala, Uganda added a third to make sure of their place in Group E, with the hosts forced to play with 10 men for the final 10 minutes after Karamoko Traore was sent off.
