Glenn Maxwell was dropped from the original squad in favour of Chris Lynn in what was seen as a shot across the bows, followed by a rebuke over his training methods from captain Steve Smith.
Two goals from Lucas Vazquez were enough to secure a 5-2 aggregate win despite a Real side, who were without Cristiano Ronaldo and Gareth Bale, being held to a 2-2 draw by second-tier Numancia.
The 21-year-old is in hot water after a video emerged of him dancing and screaming at a flat in Soho, allegedly filmed at 2.37am the day before the FA Cup third-round loss.