The two have played together more regularly this season following a long layoff for Antonio Cassano, who underwent minor heart surgery in November, and the inconsistent form of Pato's fellow Brazilian Robinho.
Pato decided to stay at Milan in preference to joining Paris Saint-Germain last week and the pair are likely to form the striking partnership for the rest of the season as Milan chase the Serie A and Champions League titles.
"There is no problem between Pato and Ibrahimovic and in general between any of the forwards," Allegri told reporters, two days after their surprise 1-0 defeat by neighbours Inter.
"It's just a case of their needing a better understanding."
"It will get better the more they play together. I was happy with Pato's performance on Sunday, I had been looking for 60 intense minutes from him and he did that.
"He just needs to re-find his scoring touch and he will be an important player for the second half of the season. Pato has indisputable quality."
Allegri also shrugged off suggestions that Milan's defeat, which left them one point behind leaders Juventus as the season approaches the halfway mark, would have any long-terms effects.
"The derby is an important game but, no matter how important it is, it absolutely doesn't change the value of Milan," he said.
"In the last 12 games before that one, we had 10 wins and two draws, conceding few goals and playing good football.
"Sunday's game was rough, tough and we paid heavily for a mistake but it doesn't diminish the value of this team at all.
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