Tooth’s departure, along with assistant Phil Male and coach Craig Milligan was confirmed on Monday night.
The coaching team handed in their resignations two days after the club’s exit in the FA Trophy, with the Royals having lost 5-1 at Ashton United.
They left with Sutton lying 16th in the Northern Premier League Midlands League, having won twice in 14 league games this season.
In a statement, Sutton Coldfield Town said: “The club chairman Nick Thurston met this evening with first team manager Neil Tooth and his coaching team Craig Milligan and Phil Male.
"It is with regret we must announce their joint resignation with immediate effect.
“They collectively feel that with the resources the club has at it’s disposal and the poor position in the league, they have taken the football team as far as they can and feel that in the best interests of the club a change is necessary.
“The chairman expressed his disappointment with their decision and thanked them for their efforts in what has been a difficult season so far.”
Ross Thorpe has been named as interim manager, while the club is currently accepting applications.
Tooth said the trio leave with their heads held high.
In a statement, he added: “Anyone who knows me will know that walking away from my club was not an easy decision to make.
“Results on the pitch have not been good enough this season and although as a management team we had the confidence to turn it around unfortunately we didn’t have the desire.
"As a manager and management team we pride ourselves on our high standards both on and off the pitch but this season some of those standards off the pitch have been no where near the level expected and we feel that this has affected our ability to keep players at the club and also bring new ones in.
“I will be forever grateful to Nick as I know how hard he has worked to keep this club alive and as a chairman he has been fantastic.
"We all want this club to do well and we honestly believe that us walking away will give them enough time to recruit a manager that can come in and start from scratch as we leave them a very talented group of players.”