The court ruled that the deal between Real and the Madrid council, which would allow land adjacent to the stadium to be incorporated into the stadium overhaul, should be suspended because the European Commission is examining it for possible illegal state aid.
The Commission said in December when it announced its investigation that the property deal appeared "very advantageous".
"The court is adopting the (suspension) measure due to the launching of a process by the European Commission relating to possible state aid given to Real Madrid," the Madrid court said in a statement.
Real did not immediately respond to an emailed request for comment on the court's ruling.
Real Madrid, which is the world's richest club by income, chose a design led by German architects GMP for the remodelling of the Bernabeu at an estimated cost of 400 million euros (USD537 million).
The club hopes the work, which would see a striking new roof and exterior added to the current structure and include a hotel and a shopping centre, can be completed by 2017.
By remodelling the stadium, which was opened in the 1950s and holds just over 80,000 spectators, Real Madrid are looking to increase match day revenue, one of their key income streams.

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