Ceballos set up Vinicius to pull the first back for Madrid and it put the wind in their sails.
Asensio drilled a low free-kick under the wall but Philip Jorgensen was level as Los Blancos pressed for an equaliser.
The Danish stopper crossed Karim Benzema’s header moments later, but Militão pounced on the rebound to level.
With the clock ticking down towards extra time, Ceballos struck with a low effort from the edge of the box, set up by Asensio, to complete the rescue mission.
“The team knew how to stay alive in games and luckily we can change that,” match-winner Ceballos told Teledeporte.
“We want to dominate matches and recently we haven’t been able to do that, we have had too many games in a row, many players coming back from the World Cup, and now we will improve.”