The 68-year-old - who previously led the club to the Vanarama National League South title in 2019 - leaves by mutual consent.
Tuesday's goalless draw at Farnborough left the Gulls winless in seven League games and sitting 11th in the National League South.
Aaron Downes will take temporary charge of the club in the interim period.
"Following discussions between both parties earlier today, Johnson’s departure as United manager was agreed by mutual consent," the club's announcement read.
"Everyone at Torquay United AFC would like to place on record its sincere thanks for all of Gary’s hard work during his time at Plainmoor."
A statement from the departing Johnson read: "After discussions today with the Football Club, we have mutually agreed that I should leave Torquay United with immediate effect.
"I have enjoyed most of my five and a half year tenure, but given the current situation, both parties agreed to part ways. I thank the players, the football staff, the office staff, as well as the Chairman & Directors for their support over this time.
"I wish the Club all the best for the future."