Young Mexican fighter Ceja was the favourite going into the fight and looked like he had done just enough to take a decision but it was McDonnell's hand that was raised at the end after a fight that took place in cold, outdoor conditions at the Keepmoat Stadium.
At the end of a tight contest, scorecards of 114-114 and 115-113 (for McDonnell) seemed debatable but plausible but the real controversy came when it was revealed that one judge scored the fight 118-110 for McDonnell.
"Oh my god, what an amazing feeling," said McDonnell, whose career appeared to be in tatters five years ago when he lost two fights in a row.
"In the first five rounds or so I felt him out and wanted to come on stronger as the fight went on.
"I started digging him in the last few rounds and I felt I could have even got the stoppage.
"I was actually enjoying it. He had a big record with 22 knockouts but I dug in because I wanted this belt. I controlled that fight."
Promoter Dennis Hobson added: "It's great, he's a special talent. He is the most successful sportsman in Doncaster. It's a special achievement. The best thing is he's still improving, how scary is that?''
The 27-year-old now has a record of 20-2-1 while it was Ceja's first defeat after he had won his first 24 pro fight – 22 by way of knockout.
On the undercard, Stuey Hall won the IBF intercontinental bantamweight belt by beating Sergio Perales thanks to a unanimous points decision.
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