Allegri hails 'world class' Khedira
Khedira provided the cross for substitute Juan Cuadrado to restore the hosts' lead in the 79th minute before sealing three points himself with a well-taken third late in normal time.
Leonardo Bonucci had earlier cancelled out Paulo Dybala's opener and the Rossoneri looked on track to earn a point in an away match at Juventus for the first time since 2011, before Khedira helped swing the match back in Juve's favour.
The Bianconeri are now four points clear of second-placed Napoli and well on track for a seventh straight Scudetto.
"Khedira is a world-class player and he knows how to read the crucial moments of a match," Allegri told Mediaset Premium.
"That is very important as in some moments you need certain players and at others you can change and introduce substitutes who can turn it around.
"We really could have done with a player like Khedira [in the draw] against SPAL as he is so intelligent. At times he might seem slow or error-prone, but he reads the game so well."
7 - Sami #Khedira has scored 7 goals in the current Serie A, his joint-record in a single campaign in his career (7 also for Stoccarda 2008/09). Thrust. #JuveMilan
— OptaPaolo (@OptaPaolo) March 31, 2018
Juve's next assignment is a visit from Real Madrid in the first leg of their Champions League quarter-final clash on Tuesday.
Allegri believes the victory over Gennaro Gattuso's side serves as a message to their upcoming opponents.
"It was important to get back to winning ways against Milan, who are in good shape," he said.
"The lads did well to bring the result home in a difficult fixture and to increase our lead at the top of the table. Wins like this send a signal."