Cristian Romero and Dominic Solanke struck Tottenham's goals before halftime. Dortmund were down to ten men on 25 minutes after Daniel Svensson was sent off for a high challenge.
Kovac stated afterwards: "Congratulations to Tottenham for the victory. In the first half we did not play well.
"We were too passive. In the second half with ten players we played much better and showed more aggression. It wasn't enough for us to win a point and we have to accept the defeat.
"It's not easy to explain. You know the position I used to play in and I expect the same from my players. We have to fight our way into the game in the Champions League and we didn't do it.
"If you play against an opponent who is vulnerable and don't bring that physicality with you, it'll make it very difficult for you."