The Brewers have claimed just a single point in seven matches through a 4-4 draw with Accrington in mid-August, since which they have lost four-successive league games.
Dino Maamria will take charge of first-team matters following the Dutch manager's departure, beginning with Saturday's home clash against Fleetwood.
"I have taken the club as far as I can with the limited resources available and it is time for someone else to come in and inject some new energy," Hasselbaink told the club's website.
"I would like to thank the fans and everyone associated with the club, including the chairman and to wish them all the best in the future."
Hasselbaink steered Burton to successive mid-table finishes following his appointment in January 2021 but the former Holland striker has presided over a dire sequence of results this season.
"I have enjoyed working with Jimmy who is an inspirational coach and I understand and respect his decision to move on," chairman Ben Robinson said.
"I want to thank him for the success he brought to the club both on and off the field and I wish him well with his future career."