The Dons have taken the decision after the team exited the Scottish Cup on Saturday, going down 2-1 at Motherwell.
A statement confirming the departure said: “Stephen has left the Dons with immediate effect alongside coaches Allan Russell and Henry Apaloo.
“The club would like to thank Stephen, Allan and Henry for their efforts and wish them the best in their future careers.
“The process to appoint a new manager will commence immediately and a further update regarding the club’s interim coaching team will be communicated shortly.”
Supporters in the away end vented their anger and frustration at the players and management team following the full-time whistle as the team made their way back to the away dressing room.
Pressure had been mounting on Glass with Aberdeen having slipped to ninth in the Premiership. They had won just once in seven games since returning from the winter break, a 3-0 win over League Two side Edinburgh City.
The former Dons, Newcastle United and Hibs midfielder had replaced Derek McInnes back in March.
Across his 41 matches in charge he had won just 14, losing 20.
The Evening Express report Barry Robson and Neil Simpson taking charge of Tuesday's match against St Johnstone.
Looking further ahead possible candidates include former Hibs boss Jack Ross, ex-Celtic manager Neil Lennon and St Mirren’s Jim Goodwin who has the Buddies challenging for fourth.
Within the club, Scott Brown is another possible option and was part of Glass’ coaching staff.