A Real win would have put them level on 85 points with second-placed Barca, who drew 2-2 at Getafe on Saturday, with a game in hand but they stayed third on 83 points with three games left.
Atletico, who like Barca have two matches remaining including the meeting between the teams at the Nou Camp on the final day of the season, are top on 88 points after they lost 2-0 at Levante earlier on Sunday.
Valencia took a surprise lead in the 44th minute at the Bernabeu when Jeremy Mathieu nodded in a Dani Parejo corner before Sergio Ramos levelled with another header in the 59th.
Parejo, a former Real player, smashed in a loose ball to restore the visitors' lead six minutes later as Valencia looked to become the first team to win at both Real and Barca in the same season since Real Mallorca in 2002-03.
But Ronaldo produced a brilliant piece of skill to volley in Angel Di Maria's centre in the second minute of added time and salvage a point for the home side.
(Reporting by Iain Rogers, editing by Ed Osmond)
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