The pardon came after his meeting with his Ethiopian counterpart Sahle-Work Zewde, who is on an official tour of Tanzania.
He will answer to nine charges related to financing terrorism, armed robbery, abduction, arson, attempted murder, assault, and battery.
Almost 7,000 people have been displaced and over 5,000 houses destroyed or damaged.
Last week, he tightened mask wearing rules.
Nairobi said the fighting is likely to create a security crisis for Kenya.