Chiellini came off after 25 minutes of Juve's shock defeat in the Coppa Italia with the score then tied at 0-0.
The centre-back was replaced by Joao Cancelo, who slotted in at right-back, while Mattia De Sciglio was forced to play alongside Daniele Rugani in the heart of defence.
This make-shift back four endured a tough night against Atalanta and ended up on the long side of a 3-0 scoreline, thanks to Timothy Castagne’s first-half strike and Duvan Zapata’s double.
The evening was only compounded by Chiellini’s injury, with many suspecting a serious calf strain. However, following the match Allegri moved to calm those fears, adding Martin Caceres would be available if the 34-year-old was sidelined.
"Let's see," he told JTV.
"He has a discomfort on the outer calf. It should not be anything to worry about, otherwise there will be Caceres.”
The Uruguayan defender rejoined Juventus this month on loan from Serie A rivals Lazio, for what will be his third spell at the club,
His introduction could prove to be hugely significant with Juventus so short on defensive options.
Both Leonardo Bonucci and Andrea Barazagli are ruled out through injury, meaning Caceres and Rugani are the squad’s only fit centre-backs.
Given the lack of options available to Allegri, he has linked with a deadline-day move for Parma defender Bruno Alves.
It remains to be seen whether Chiellini will be available for Juve’s next clash, when they host Alves’ Parma in Serie A on Saturday.
The reigning Italian champions will want to bounce back quickly from Wednesday’s humiliation. The defeat was the first time that Juventus have lost a Coppa Italia tie for five season and the first time they have been knocked-out before the quarter-final stage since 2006/07, when the club were in Serie B.
Worrying, the Bianconeri’s league form has also taken something of a hit in recent weeks and they only won by the narrowest of margins last time against Lazio, when two goals in the last 20 minutes ensured Juve ran out as 2-1 winners.