The Irishman sealed the club's return to the level for the first time in 32 years.
He took the team to the 2019/20 National League South title – and started this season in impressive form.
But their great start faded, and the Stones have won just once since the second week in November.
Brennan left Grosvenor Vale hours after Tuesday night's match with Maidenhead United was postponed.
The club lost their four previous matches against Altrincham, Aldershot Town, Hartlepool United and Maidenhead United.
A club statement read: "The club wishes to share that as of this evening, Dean Brennan has left his position of first team manager at the club.
"Stuart Maynard will take charge of the side for the FA Trophy game at Darlington on Saturday.
"We wish to place on record our thanks for everything Dean has achieved in his time at the club and wish him every success in the future."
PHOTO: Alan Palmer