The vote was 58 in favor and 3 opposed.
Kerimkulov previously served as the mayor of the Kyrgyz capital Bishkek.
Last month, parliament rejected Bakiev's first choice for the post, Daniyar Usenov, saying that his business interests could conflict with those of the country.
The legislature has rejected several of the president's candidates for government posts, forcing him to submit new nominations.
(with material from Interfax)