The League One side have won just one of their last five games, picking up only four points from the 15 on offer in that time.
That run has left them 16th in the table with 16 points from their opening 13 games, having won four, drawn four and lost five matches so far this term.
Barton's final match in charge was Tuesday's 1-1 draw at home to Stevenage, when Chris Martin rescued a point with an 83rd-minute equaliser.
Andy Mangan will take over the reins as interim boss while they search for a permanent replacement.
"Bristol Rovers Football Club can confirm that today the club has relieved first team manager Joey Barton of his duties," read a statement on the club's website.
"Everyone at the club would like to thank Joey for all his efforts and wish him well in the future.
"In the interim, Andy Mangan will lead the team supported by Glenn Whelan, Danny Ventre and Anssi Jaakkola who will remain in post."
Barton joined Bristol Rovers in February 2021 having previously been in charge at Fleetwood Town.
The former Manchester City and Newcastle United midfielder oversaw 143 games as Rovers boss, winning 53 of those and earning promotion from League Two in his first season at the helm.
Mangan's first game in interim charge will come on Saturday when his side host Northampton Town.