Berg presided over a third defeat in four winless matches before Blackburn's lowest home crowd of the season after Craig Bellamy restored City's lead in the 54th minute after Josh King had briefly brought Rovers level.
Heidar Helguson laid on goals for substitutes Lee Mason and Kim Bo-Kyung as the Bluebirds made it five wins in six unbeaten games.
"We are disappointed to lose another game at home," said Berg, who insisted Rovers' target for the season remained promotion even though results on Saturday could leave them seven points from the play-off places.
"We think Cardiff were the better team all over, although maybe not as much as the scoreline suggested, but you can't have any complaints.
"They were more experienced than us, they had far better finishing and they also defended better than us - I think that was the key in this game.
"We were not happy with the way we defended - we can defend much better than we did and, also, the way we used the ball in the first half is a little bit of a way off where we want to be.
"We can play better than this."