The 22-year-old midfielder was reportedly in great distress when he was carried from the training track on Thursday.
The club confirmed it was not a structural injury and he will only require a "two to four week rehabilitation program".
Morabito has already undergone three knee reconstructions since making his AFL debut in 2010.
He first ruptured his ACL in the pre-season of 2011 and missed the entire year.
Morabito fought back to play one WAFL reserves and seven WAFL league matches for Peel Thunder in 2012 before rupturing his ACL again in July of that year.
He then re-injured the same ACL at pre-season training in January 2013.
The most recent reconstruction was a LARS procedure.
He trained through the latter stages of 2013 but did not play until returning to the WAFL for the start of the 2014 season.
Following 11 matches with Peel, Morabito made his long-awaited comeback to the AFL in round 16 against Melbourne in Darwin, his first AFL game since the 2010 semi-final.
Morabito played three games before being sent back to the WAFL and coach Ross Lyon rated him an outside chance to play this week against Port Adelaide.
The injury-prone midfielder has played just 26 matches for Fremantle since he was drafted in the 2009 NAB AFL Draft.
Morabito signed a one-year contract extension last month to remain at the Dockers in 2015.
