Kim Thomas Riley, 27, made a getaway from Royal Darwin Hospital, where he was undergoing assessment for chest pains.
Authorities found him hiding under a log near Cape Crawford, a remote road stop in the Northern Territory outback.
Police arrested him "without incident" after a two-day search.
His partner, Rachel Chatfield, was charged with aiding his escape.
Police said she picked up Riley from the hospital and the couple drove more than 700km south to the small town of Elliot.
Riley reportedly left Ms Chatfield and her children on the side of the Stuart Highway for reasons that are not yet clear and drove several hundred kilometres east.
The car he was driving ran out of petrol at Borroloola, a remote fishing community on the Gulf of Carpentaria.
He was arrested about two kilometres away at Cape Crawford, still wearing handcuffs and with an injury to his foot.
A prisoner who escaped from hospital in northern Australia was rearrested about 1,000km (620 miles) away still wearing handcuffs.