Ichi Ban crossed the finish line on Thursday morning behind seven other yachts.
Comanche won line honours after Wild Oats XI was penalised by an hour for breaking race rules.
Allen said it was a fast and challenging race.
"We had water coming over the whole boat, we had water coming over our heads, we were buried in water for a long time," he said.
"Spinnaker damage really did slow us down.
"Then we took some time off the boats around us coming down the coast into Storm Bay, and then we parked up again [and had] 20 minutes of doing nothing, watching the time tick away and thinking about how we could not get across Storm Bay last year.
"That made us pretty nervous and pretty tense.
"It was an amazingly quick race. It is incredible that you could do it this fast in a 52-footer. It was some of the most exhilarating sailing I have ever done.
"The best sailing conditions I have ever seen. This is my 28th race and I have never seen it this good."
Ichi Ban entered the Derwent ahead of Quest, Hollywood Boulevard and Mascalzone Latino to take the handicap lead.
Quest skipper Bob Steel, who had been another favourite to take out the overall title, said Allen deserved to win.
"It's his 28th Hobart," he said.
"I've had my share, so I am jubilantly disappointed for us but happy for Matt."
The overall winner will be officially announced at 12:00pm.
Wild Oats XI crossed the finish first but was found to have breached the rules over a tacking manoeuvre at the start of the race.
Comanche crossed the line in second place nearly 27 minutes after Wild Oats XI.
International jury chairman John Rountree said because of the breach of race rules — which are the International Racing Rules of Sailing under which the race was being conducted — Wild Oats XI was penalised one hour.
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