The visitors were hard to handle in the opening 10 minutes with Matheus Alias having a crack at the goals forcing Kaylor Navas into a save.
Zinedine Zidane’s charges were quiet after 20 minutes as Fuenlabrada kept on pushing for the opening goal.
Luis Milla found the surprising breakthrough with a thunderous strike in the 25th minute following a corner to stun the home fans, 0-1.
Los Blancos who had made a host of changes for this encounter were not getting into the match and it was a scrappy affair after 35 minutes.
Dani Ceballos had the first real chance for the hosts in the 40th minute but rushed his move on the edge of the box to send the ball over the bar.
Fuenlabrada were leading 1-0 at halftime but Madrid held a 2-0 win from the first leg and were still comfortable with a 2-1 aggregate lead.
The visitors were defensive when they turned up for the second half and Zidane turned the game on it’s head by introducing Gareth Bale in the 62nd minute.
Bale made an immediate impact providing a sublime cross moments later into the box that was converted by Borja Mayoral for the equaliser, 1-1.
Bale was again heavily involved in the second goal in the 70th minute as his strike was parried away by goalkeeper Pol Freixanet but only into the path of Mayoral, who rounded the shot-stopper for his second goal in eight minutes, 2-1.
The visitors upped their efforts with 10 minutes left on the clock. They were certainly rewarded as Portilla restored parity a minutes before time to make it 2-2.
However, Madrid controlled the match in stoppage time to run out 4-2 winners on aggregate.