The former Bradford City midfielder, 36, had managed the team since 2013 and led the club to promotion in May 2015 before a 20th-placed finish last term.
"Struggling at the foot of the National League table, the board felt a change was necessary," a club statement said.
Bower's assistant, Danny Boshell, has also been dismissed, with defender Adam Lockwood taking interim charge.
National League Guiseley have parted company with manager Mark Bower after starting the season with five defeats.