Ajax have not beaten Madrid in 24 years and thought they were on their way at the Johan Cruyff Arena when Nicolas Tagliafico headed home after a Thibaut Courtois error.
Madrid was already without Gareth Bale, Toni Kroos, Marco Asensio, Mariano Diaz and goalkeeper Thibaut Courtois due to injury.
Cengiz Under sent the ball over the bar from point-blank range with Thibaut Courtois already down on the ground in first-half added time and two defensive blunders led to Gareth Bale's goal.
Chelsea goalkeeper Thibaut Courtois believes the FA Cup winners need to spend heavily if they are to challenge for the Premier League title next season.
Thibaut Courtois faces a defining period as the Chelsea goalkeeper juggles his bids for FA Cup and World Cup glory.
Courtois announced via his Facebook page on Tuesday night that he would be taking action along with his father after comments made by Wilmots.