Portugal have been consigned to the play-offs and will have to wait until March next year to see if they will play at the Mundial.
Renato Sanches had given the hosts the lead after only two minutes but Dusan Tadic equalised for the visitors before half time and substitute Aleksandar Mitrovic snatched all three points at the death to send Serbia through to the World Cup at Portugal’s expense.
Reflecting on the defeat, Santos said: “It looked like it was going to be, but it wasn't. We scored the goal, we had the initial moments. But then we started to drop deep a lot.
“The players tried. But then we didn't turn the game on. Every time we did, we created problems. But most of the time we couldn't.
"Serbia were better. We tried. Our DNA is to have the ball on our feet and play. Bernardo Silva wanted the ball, but he was the only one. We played with fear and anxiety. It's my responsibility."
When asked about the prospect of the play-offs, Santos added: “We'll be in Qatar. We know we didn't do what we should, but we'll be there.
“We've always played to win and think about the offensive moment. But it doesn't always turn out as we want. And it's my responsibility."
Portugal will get to know their opponents for the play-offs on November 26.
