City surrendered a lead to crash to a 3-1 defeat at the Amsterdam ArenA which left them bottom of Group D with three matches to play.
The Italian said: "They were better than us. They played better football. It is my fault, I didn't prepare well for the game and I take the blame."
He added: "I thought in one way and it was different. When you prepare in one way and it is a different game it is difficult. We had more chances to score and in the Champions League you need to score. It is my fault, I repeat."
It is not the first time Mancini has sought to remove the pressure from his players in this way.
Last season he was critical of himself after a Barclays Premier League loss at Everton and again after being eliminated from the Europa League by Sporting Lisbon.
City started sluggishly in the Dutch capital but took control with a fine Samir Nasri strike. They failed to build on their lead and were pegged back by Siem de Jong before Niklas Moisander and Christian Eriksen, with aid of a deflection, made sure of victory for the hosts.
Mancini varied his tactics and formations as he chased the game and at one stage had Gael Clichy, who had the unlucky final touch on Eriksen's strike, playing in an unfamiliar centre-back role.
Defender Micah Richards told Sky Sports: "It's not something that we've worked on a lot, we're just used to a back four. But the manager likes it and if we want to do well with it then we'll have to work harder on it.
"It's a hard system and I think the players prefer a 4-4-2 but he's the manager and we'll do what he says."
Source: PA
Source: PA