Kenya's health secretary said Kenyans and medical workers flying in from those states would still be allowed in.
Kenyan Airways says it will stop flights to Liberia and Sierra Leone when the ban comes in on Wednesday.
The World Health Organisation (WHO) says Kenya is at "high risk" from Ebola because it is a major transport hub.
The epidemic began in Guinea in February and has since spread to Liberia, Sierra Leone and Nigeria.
On Friday, the death toll rose to 1,145 after the WHO said 76 new deaths had been reported in the two days to 13 August. There have been 2,127 cases reported in total.Earlier, Kenya's health ministry said four suspected cases of Ebola in the country had tested negative for the virus.
The cases had involved a Liberian national and two Nigerians who had recently travelled to Kenya as well as a Zimbabwean.
Kenyan Airways said it had decided to cancel flights to Liberia and Sierra Leone's capitals after advice from Kenya's government.
It said all passengers booked on the suspended flights would get a full refund.
The company said its flights to Nigeria were not affected by the suspension.
'Strict checks'Announcing the government's decision, Kenyan Health Minister James Macharia said it was "in the interest of public health".
He warned that Kenyans and health workers who had returned from the three west African states would face "strict checks" and would be quarantined if necessary.
On Friday, medical charity Medecins Sans Frontieres (MSF) said the outbreak would take at least six months to bring under control.
MSF President Joanne Liu said the situation was "deteriorating faster, and moving faster, than we can respond to".
The WHO also admitted that the scale of the outbreak appeared to be "vastly underestimated" and said "extraordinary measures" were needed to contain it.
Ebola is transmitted by direct contact with the body fluids of a person who is infected.
Initial flu-like symptoms can lead to external haemorrhaging from areas such as eyes and gums, and internal bleeding which can lead to organ failure.
The WHO says the risk of transmission of Ebola during air travel remains low.
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