The club have appointed the 41-year-old the permanent boss following his spell in a caretaker role last season following the departure of Michael Appleton
The 41-year-old took over as caretaker manager following the departure of Michael Appleton in March and has now been handed the role on a permanent basis.
Bowyer has been with the club since joining in 2004 to take charge of the Under-18 side and could not hide his delight at the appointment.
"It is a huge honour and a proud moment for me," he told the club's official website.
"I have been at the club for nine years, I know the traditions. The foundation of the club was built on hard work and that is what we need to produce.
"The supporters want to see the players out there playing for the shirt and giving it their all. We need the players to show the same passion that the fans gave us during our last six games where we just lost the once."
Managing director Derek Shaw added that he felt Bowyer's work with the club's youth would help him in his new role and praised his work last season as he helped guide the team to safety and a 17th place finish.
"In the two spells as caretaker manager Gary achieved approaching two points a game," he added.
"He has the respect of the players and we feel his in-depth knowledge of working with the youngsters will be of great benefit to Rovers.
"He is held in high regard in football and we certainly wish him all the best going forward."