David Mearns, dubbed "the shipwreck hunter", led a privately-funded funded search operation for the aircraft on behalf of the family of the player, who had just signed for Cardiff City.
The plane had requested permission to land before losing contact with Jersey air traffic control.
An official search operation began but was called off on 24 January, after David Barker, Guernsey’s harbour master, said there was only an “extremely remote” chance that the men had survived.
A subsequent campaign raised £260,000 for the private search, which began early on Sunday morning.
Mr Mearns, the director of Blue Water Recoveries, led a team on one search vessel, while the UK Air Accidents Investigation Branch (AAIB) also sent a team aboard another vessel.
The marine scientist confirmed the wreck may contain the missing men's bodies.
"That's a possibility," he said.
The privately-funded search team immediately called in the AAIB and stood down once they found the plane, he added.
“The biggest surprise, to both of us, was that most of the plane is there. It is broken but most of it is there.”
Any further steps, including the recovery of the plane, are likely to be led by the AAIB.
“Now we’re talking about an accident scene,” Mr Mearns said.
“It’s no place for a privately funded recovery attempt.”
The scientist claims to have located 24 major shipwrecks in his career, including the HMS Hood.
He told the BBC that wintertime conditions will likely complicate the plane’s recovery.
Mr Sala and Mr Ibbotson’s families were informed about the wreck’s discovery.
“Our sole thoughts are with the families and friends of Emiliano and David,” Mr Mearns said on Twitter.
Additional reporting by agencies
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