Luciano Spalletti's side recorded an emphatic 4-1 victory over Fiorentina on Friday to move back to within five points of the champions at the top of the table and extend their run to seven league wins in a row since their loss in Turin in January.
Allegri is not surprised by Roma's impressive form since Rudi Garcia was replaced as head coach and believes their 1-0 victory over the capital club could prove crucial as the season enters the closing stages.
"It's not surprising at all because Roma are a high-quality team and are still one of the candidates to win the Scudetto," he told reporters.
"The win we had against Roma was crucial, as it allows us to be five points clear of them with a game in hand.
"It won't be easy and we must either maintain this three-point gap or even increase it over the upcoming mini-tournament of 11 rounds.
"All we have to focus on right now is winning, as that will guarantee we are at least three points clear of Napoli."
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Juve reached the Coppa Italia final after a penalty shoot-out win over Inter, who recorded a shock 3-0 victory to take the tie into extra-time and spot-kicks, but Allegri feels the result could prove an important wake-up call.
"Let's say Wednesday's defeat was healthy from a mental point of view, because we reached 21 games without losing and it was a painless loss because we achieved the goal of reaching the final," he said.
"The game tomorrow will be very different. It will be very difficult because Atalanta are a team who do well in home matches, so we have to be good. But we go there with one aim - to win."
Allegri confirmed that Claudio Marchisio is available for Sunday's clash but does not expect Giorgio Chiellini - who limped out of the Coppa clash this week - to return to action before the second leg of the Champions League last-16 tie with Bayern Munich.
"Marchisio is okay, he's ready to play. [Stefano] Sturaro has a problem with his toe, so it's impossible to take him. The others are all available," he added.
"Chiellini is making progress, we'll see if he'll be ready in a week. For Sassuolo it'll be very difficult."