The shock result in Norway came as a largely second-string Roma side crumbled woefully, although it still sit second in Group C after three games.
It was the first time in his 1,008-game coaching career that Mourinho has seen one of his teams concede six goals.
Mourinho said he expected more from his players, but told reporters they now knew why he usually selected the same group for games, rather than being a coach who rotates his squad.
On the night when his former team Tottenham also lost in the competition, Mourinho was left to accept responsibility for his Serie A outfit's embarrassing away trip.
"I decided to play with this team. The responsibility is mine," he said. "Obviously I had done it with a good, double intention. On the one hand, giving an opportunity to people who work a lot and don't play a lot. On the other hand, consider our squad and all the games we have to play, I let people who play practically always have a rest.
"Then, we lost against a team who have more qualities than us. It's simple. The main Bodo team is better than ours who started the game.
"If I could always play with the same men, I would. I believe that doing so is a great risk, however. In a group-stage game, with six games and six points already acquired and two more games to play in Rome, I decided to make these changes.
"I knew about the limitations of some of our players, it's nothing new, but obviously I expected a better response. But as the decision is mine, so is the responsibility."
Bodo/Glimt lead the way in the Norwegian Elitserien, and Mourinho saw his team go into half-time trailing 2-1, with a flurry of second-half goals showing the Portuguese the limitations of his fringe players.
Mourinho said: "I had never hidden it, I knew that the team had many limits. The good thing is that now at least none of you will ask me why I always play the same players."
Two-time Champions League winner Mourinho said Roma would face pace-setter Napoli in Serie A on Monday (AEDT) "with the weight of a defeat that I would define as historic".