The striker's goal was allowed to stand despite a collision with defender Pepe.
Costa ran into the Portuguese centre back in the build-up to his equaliser in the 24th minute to cancel out Cristiano Ronaldo's fourth minute penalty.
Italian referee Gianluca Rocchi gave the goal after consulting the VAR team.
The system, which was trialled in Germany's Bundesliga and Italy's Serie A last season, allows the video assistant to review decisions where a “clear and obvious” error is spotted.
Later in the first half Spain midfielder Isco asked Rocchi to consult the video assistant again when a shot from Andres Iniesta came flying off the underside of the bar but the Italian indicated he would have received a signal on his watch from the goal line technology being used had the ball crossed the line.
(Reporting by Richard Martin, editing by Pritha Sarkar)
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