Acosta was leading the race on lap 12 of 24 when his bike suddenly lost power on the straight near turn 10 and the Spaniard desperately tried to warn the riders behind him.
However, second-placed Marquez had no time to react, hitting the back of the KTM before he and his Ducati bike went towards the wall and then cartwheeled through the air.
The wheel from Marquez's bike also hit VR46 Racing's Fabio Di Giannantonio who went down.
The medical team confirmed all riders were conscious but Marquez was taken away in an ambulance and would not be involved in the restart.
Race directors said the race would be restarted for 13 laps with grid positions based on the standings as of lap 11.