Kean was an unused substitute for the first leg, which ended in a 1-1 draw in Amsterdam after David Neres cancelled out Cristiano Ronaldo's headed opener.
Ronaldo was rested for Saturday's league game at SPAL, with Mario Mandzukic also given the day off as Allegri made wholesale changes ahead of Tuesday's second leg against Ajax in Turin.
And naming an experimental young team backfired as SPAL came from behind to win 2-1, meaning Juve must wait to clinch an eighth consecutive title.
It would have been the quickest Serie A title triumph ever had they got a point on Saturday, but despite Kean giving Juve a first-half lead, Kevin Bonifazi and Sergio Floccari struck to deny the Bianconeri a slice of history.
And Allegri accepted the 19-year-old is pushing hard to be selected against Ajax, with Mandzukic having been preferred as Ronaldo's support act in the first leg.
"Kean was feeling a little tired, so I preferred to take him off," Allegri told Sky Sport Italia.
"When he starts moving wide and doesn't attack the goal as much, that means it's time to take him off the field.
"He has different characteristics to Mandzukic, but obviously having him in this shape is important and I'll evaluate what to do on Tuesday."
Allegri defended making so many changes to his side, noting Ajax was the priority with the league title an inevitability.
"It would have been easy to field the first choice XI today and get the Scudetto," he added. "But we've had such a remarkable run of results this season that it was more important to focus on the Champions League game coming up.
"The key to Juventus winning the Scudetto is that we do well in the head-to-head clashes, but above all bring home the points everywhere else.
"You usually win the Scudetto with 84 to 86 points, but last term Napoli had 91 – a club record – and still finished second, so our performance that season was extraordinary.
"We had a lot of young players and they did well, but above all the second goal showed a lack of experience.
"I needed to see the conditions of Juan Cuadrado, who is unfortunately off the Champions League squad list, and also [Paulo] Dybala, whose fitness levels weren't at their best. The more he plays, the better shape he gets into.
"He rediscovered some enthusiasm today and it wasn't easy for him psychologically of late to have only 20 minutes or so and then get hurt again."