We forced the Italians on the back foot in the first half and eventually took the lead 10 minutes into the second half when Fredi Kanoute guided home Johnnie Jackson's cross.
Fredi had another chance immediately after his goal but Cagliari hit back with two goals in two minutes to clinch victory.
"We played well in the first half," said Head Coach Jacques. "We defended together and had three or four situations to score.
"The first half, for me, was good from my team.
"It's never easy to lose a game and I was disappointed to concede the first goal because I've told the players it's dangerous to lose the ball 20, 25 metres from goal. When we play a good team it will always be a goal.
"After the games against Rangers and Feyenoord I'm disappointed we conceded like that."
Jacques Santini took encouragement from our first half display against Cagliari but was disappointed with the goals conceded in Saturday's 2-1 friendly defeat.