The Argentine last played on the ATP World Tour in February 2014 before a recurrence of a wrist injury, which required surgery.
Del Potro, US Open champion in 2009, was expected to open his season in Queensland with an injury-protected ranking.
He has slipped to number 137 in the world due to his inactivity.
But the Brisbane International confirmed on Twitter on Thursday that Del Potro had withdrawn.
It puts question marks over Del Potro's participation at the Australian Open, which starts on January 19.
The withdrawal is another blow for the ATP 250 event in Brisbane, with Croatian US Open winner Marin Cilic having also pulled out.