The pair, in their 40s, were spotted by a rescue jet on Sunday, more than 25km south of their dive site off North Stradbroke Island.
Acting Sergeant Matt Boswell said it was a relief to find the two men safe and well.
"It's a great outcome," the officer in charge of the Dunwich Police Station told reporters.
The 45-year-old from the Brisbane area and 43-year-old from the Gold Coast were found about four kilometres off Main Beach.
Police and emergency services were alerted on Saturday morning when the pair failed to return to the boat at the scheduled time.
They were finally spotted by a search and rescue jet at about 7am on Sunday.
The aircraft dropped a life raft before water police arrived and a helicopter airlifted them to safety.
The two men were taken to the Gold Coast University Hospital and have since returned home.
Acting Sergeant Boswell said the men were battling tough conditions overnight.
"Water conditions were pretty rough," he said.
"And obviously, just being out in the ocean for so long, the exposure."
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