Ola Toivonen scored from the halfway line in the third minute of stoppage time to punish a dreadful mistake from Lloris and give Sweden a 2-1 home win that puts them top of Group A, above Les Bleus on goal difference.
The Tottenham goalkeeper opted to control the ball under pressure from substitute Sebastian Larsson and subsequently miscued his clearance, allowing Toivonen to seal victory in spectacular fashion after the game appeared destined to finish level.
Deschamps revealed Lloris felt awful about his blunder after the match and knows what he did wrong, with the head coach keen to highlight that it was uncharacteristic.
"I am not going to condemn Hugo," Deschamps said to TF1. "He has often been decisive with us.
1 - Hugo Lloris has made his 1st error leading to goal with France since September 2013 v Belarus (2) in the World Cup 2014 qualifiers. Blow pic.twitter.com/w529iPCLKw— OptaJean (@OptaJean) June 9, 2017
"He preferred to control the ball. If he clears the ball far and away, there is no way it comes back. But he knows that. He knows it is his fault and it cost us.
"He is a keeper who made a mistake and it is noticed more than an outfield player. It is unfortunate for him and for the whole team. The players were extremely dejected, Hugo most of all. Losing always hurts and under these circumstances it hurts more."
Deschamps added: "It is a catastrophic scenario. If we didn't win this game, we should have got a draw. With the result level, we should have slogged through to the end.
"A draw would not have been ideal but it was a good point. We could have kept Sweden behind us, but that is no longer the case. I would have preferred a different outcome, a positive one, that would have allowed us to stay in first place.
"We still have four games - 12 points to play for - and we are going to have to battle hard to reach our goal.
"The match against Netherlands at Stade de France on August 31 was always going to be important. Now it will be even more so."
France are back in action with a home friendly against England on Tuesday.