The Gulls are out of the form in the National League South and on Saturday they went down 1-0 at home to Chippenham. They had won just once in six matches.
Owner Clarke Osborne saying it is a decision made with “great regret”.
A statement on the club's official website suggests he stepped down from his position after days of talks.
Owers kept his job despite not being unable to keep Torquay in the National League last season.
The former Bath City manager leaves Plainmoor with the club sitting in 14th place in the table after nine matches.
Osborne said: “Our decision comes after some days of discussion with Gary and from my personal standpoint, I make this announcement with regret.
“Professional football is demanding on both managers and players and it is fair that our supporters expect success on the field.
“I am sorry that despite our strenuous efforts and providing the financial resource necessary, we have not found consistency and are now behind where we expected in our intended journey to the top of this division.”
Owers said: “It is with huge regret that I leave Torquay United. I am sorry that we have not found the success that we planned for.
"Our lack of goals and strong performances do not reflect the quality of the team, its preparation and training. There are sometimes circumstances that drain confidence."
Torquay play Hungerford Town on Saturday and the club say they are working hard to find a new manager.