Buffon was sent off for his angry protests which followed the penalty decision and bitterly criticised referee Michael Oliver, saying the English official was out of his depth and had a 'garbage bin' instead of a heart.
Juve were leading 3-0 in the quarter-final, second leg, having wiped out a three-goal deficit from the first tie in Turin, but were knocked out when Cristiano Ronaldo converted to make it 3-1 and send Madrid through 4-3 on aggregate.
"The evening in Madrid has done him good, it has given him the shot of adrenaline he needed," Allegri told reporters. "That's how champions live."
However, he said that second-choice Wojciech Szczesny would play in Wednesday evening's (Thursday morning AEST) Serie A match at Crotone.
Buffon, 40, widely expected to retire at the end of the season, has been widely criticised for failing to apologise to Oliver over the outburst.
Allegri said the match with lowly Crotone will have more influence on the outcome of the title race than Sunday evening's (Monday morning AEST) match at home to second-placed Napoli.
Crotone, who last season pulled off one of the great escapes in Serie A history, are again fighting the drop and are stuck in the relegation zone, one point adrift of safety.
"Between Crotone and Napoli, the more decisive match is the one against Crotone," Allegri said. "It would be a significant advantage to reach the match against Napoli with a six-point lead.
"I have heard talk of scudetto and celebrations. We are waiting until it's mathematically won, we need more wins," he added. "Napoli have a single objective, there is more pressure on them and they will do anything to re-open the title race."
