Juve won 1-0 and survived a penalty shout in a controversial game.
Allegri said: “After going 1-0 up, we could've added another goal, or at least done better to control the ball rather than allow Cagliari opportunities to equalise.
“I will say that Cagliari did not deserve to lose today. VAR is an instrument that was meant to reduce controversy, but instead it has increased it because people don't accept the referee's decision.
There was also a bitter blow for, as Paulo Dybala limped off with a suspected hamstring strain.
“We don't know how bad it is now, but he will have tests. Fortunately we go into a two-week break now and he'll evidently need to rest more than the others during that time, so hopefully will be fresh for the final weeks of the season."