Liverpool, who beat the French side 5-1 at home last month, remain top of Group E with nine points from four matches, leading Toulouse by two points with two games to go.
"It was well deserved to lose because they won pretty much all the decisive challenges, battles," Klopp told reporters after the match.
"We have too many situations where we should have won the ball but we didn't."
It was the second disappointing result in a week for Liverpool after Sunday's draw at Luton Town but Klopp said there had been no lack of intensity from his team.
"No, I am not concerned. In the end, we were intense - we threw everything in," he added.
"But the problem is in a football game you have to make the decisive things in the right moment to do them right. We cannot concede the goals we conceded again."
Liverpool midfielder Alexis Mac Allister was denied a late equaliser due to handball, a decision Klopp protested with the referee.
"I only saw the video back now and for me, it's not a handball," Klopp said.
"The ball goes to the chest and then I don't see a contact with the arm, to be honest. Maybe they had a different picture than I had."
