Spain boss Luis Enrique said David de Gea told him he was fouled by Danny Welbeck as England were denied a late equaliser in the Nations League tie at Wembley.
England took the lead through Marcus Rashford (11) but were pegged back through close-range finishes from Saul Niguez (13) and Rodrigo (32).
The visitors had edged the game, but almost threw away three points after a late surge by England saw substitute Welbeck turn home after De Gea dropped the ball under seemingly unintentional contact from the striker.
Referee Danny Makkelie and his assistant ruled out the goal, a decision that left Harry Kane incensed as he claimed the referee "bottled it".
When Enrique was asked for his view of the decision, he replied: "I couldn't see, it was difficult, David de Gea told me he was fouled.
"When you think about the whole match, we deserved to win."
De Gea had been under severe scrutiny in Spain over whether he should keep his place in the side after an underwhelming World Cup campaign.
However, he responded with a solid performance at Wembley as he made two superb stops to deny team-mate Rashford.
Enrique said he never doubted the Manchester United goalkeeper's ability.
He said: "I'm happy with how De Gea performed. I never had doubts, his errors have helped him grow up.
"I was happy with the attitude of players throughout the game. But we must improve at the end of the game. We suffered but it's always the case against England at Wembley.
"We had our chances to kill the game off, little details make the difference."