"We are pleased to have found Cookie safe and sound after an extensive search and we look forward to reuniting him with his owners," the airline said in a statement.
"We will continue to investigate how this incident occurred and we will review and update our processes accordingly."
news.com.au understands the cat was found in a non-operational area of Brisbane airport.
Earlier, in a desperate plea on Facebook, Jessica said only Cookie's cage and a blanket arrived at the airport, but their cat was nowhere to be seen.
"We are now being told that Cookie escaped from his cage (no word on how) on the tarmac while in Brisbane," Mrs Thomas wrote on Facebook.
"I am absolutely heartbroken and just want my fur baby home."
News.com.au understood Cookie may have escaped from his crate prior to boarding the aircraft, possibly because the cage door of the enclosure wasn't secured properly and not all of the required additional cable ties were in place.
Virgin Australia was believed to have conducted at least three searches for Cookie, including resourcing additional operational team members to search the area around the airport where Cookie was last seen.
"Virgin Australia is saddened by the disappearance of Cookie," a spokesperson said in a statement to news.com.au this morning, while the cat was still missing.
"This is a distressing situation for his owners and we are providing regular updates to them.
"We are truly sorry for this incident and we are doing all we can to locate him.
"We take pride in transporting our guests' pets and our teams follow stringent guidelines to ensure the highest of safety standards are upheld. We will continue to investigate how this incident occurred and review and update our processes accordingly."
Speaking to Nine, Mrs Thomas said they were very anxious about putting their pet on a plane, and now their apprehensions are warranted.
"We were very nervous and now we realise we had reason to be," Mrs Thomas said.
"I just want my cat back."
