The Uruguayan opened the scoring in Udine, latching on to Joao Cancelo's cross and nodding in from close range ahead of Cristiano Ronaldo.
Juve's Portuguese forward added the second soon after, effectively sealing a comfortable win to extend Juve's run of successive victories to 10 in all competitions.
But it was Bentancur who caught the eye and Allegri commended his display.
"That could have been a tricky match, but we displayed immense maturity and determination," the Italian told Sky Sport Italia.
"The players know what we're working on. On occasion we've been somewhat lacking focus after taking the lead, but today [Saturday] that wasn't the case.
"Rodrigo Bentancur impressed me in midfield, both from a tactical and technical perspective, then he obviously scored the goal as well.
"Above all, I feel that we were not too rushed, but we still played the ball around quickly all over the pitch, making the most of the technical ability we have at our disposal.
"But, the international break has come at the right time, because we need a rest. We need to set new targets all the time, and now that is a sequence of clean sheets. We risk getting complacent if we don't continue setting new targets."
Cancelo was another standout performer for Juve and Allegri has been impressed with the right-back's improvement.
"Cancelo has improved a lot, technically he is extraordinary," Allegri added.
"In the first half in some situations he got caught behind, but at times he trusts his pace too much and is a little slow in starting his runs, so he needs to run at the same time as his opponent, but it is one of the steps he must take. Today he was really good."