The pair - the club's only fit senior forwards - both joined the squad as manager Manuel Pellegrini gave a training-ground talk to his players on the eve of the game.
But as the rest of the players began to train on the field - at a session open to media cameras - Aguero and Jovetic took their leave along with the injured Aleksandar Kolarov, David Silva and Edin Dzeko.
There was no indication whether either Aguero or Jovetic were injured, but their lack of involvement with the rest of the squad did raise questions.
City need a positive result against the Germans at the Etihad Stadium to maintain their interest in the competition.
Pellegrini's men have collected just two points from four Group E matches and will be eliminated if they fail to beat Bayern and there is a winner in the game between CSKA Moscow and Roma.
City had hoped Silva might be fit to play having returned to light training last week, but the Spaniard was unable to feature against Swansea on Saturday and had therefore been rated doubtful.
Source : PA
Source: PA