Goals from Harry Kane in either half and a solo effort from Christian Eriksen handed Mauricio Pochettino's side all three points, condemning the Toffees to back-to-back defeats after their loss at Chelsea last time out.
"I am disappointed," Koeman told BBC Sport afterwards. "I thought the first 25 minutes was OK. We had some chances but after [going] 1-0 down it was really difficult. We lost control in the game. Tottenham's midfield diamond was difficult to control.
"Straight away in the second half the third goal killed the confidence in our team and Tottenham grew even more.
"The frustration is the second half. I don't ask for yellow or red cards but in several situations we were too nice. We were too nice, too weak in the second half but that is also something about confidence. The key is to learn from today. We knew Tottenham are a really strong side with really strong technical players.
"I know how it works in football. If you sign some players they are losing a bit being realistic. Everyone is talking Everton top six but if you know the qualities of the players in the top six it is a challenge. We have enough games coming up to have a good reaction."
The result leaves Everton, who next travel to Atalanta in the Europa League, 15th in the Premier League table.