After the decision was made to downgrade to a single-day event, entrants were given a one-hour extension before the final weigh in at 5pm on Sunday, where a 20kg kingfish caught by Jones was crowned the winner.
The winner of the competition is decided on a points basis according to the species and weight.
MegaFish committee member and Hunting and Fishing Napier manager Dylan Woolhouse said despite limited time on the water, big fish were caught across every species.
"We had three yellow fin tuna come in, which was the first time in about 12 years - one of them was from a junior," he said. "And we had a marlin caught and weighed in at 81kg.
"But the 20kg kingfish, which after the tournament formula is taken into consideration, was what won the $10,000. It's the first time the tournament has been won by a kingfish."
Tuna species have claimed the major prize in each year since the new structure was introduced in 2016, while the biggest catch in the history of the tournament was a 417kg mako caught in 1999.
Woolhouse said it's lucky so many entrants were still keen to compete, despite the adverse conditions.
"Even with the bad forecast, the one-day produced a lot of fish," he said. "What could've been is still up for debate, but the turnout with everything considered, couldn't have been better."
Price said sea conditions improved dramatically following the cancellation of the first three days of the competition.
"The water was nicer as far as the wind was concerned. But there was still quite a good swell out there for the competitors to deal with," he said.
The competition, which was first held in 1977, reached a peak in the 1980s when more than 700 entrants took to the water chasing the biggest catches – usually sharks.
A further $40,000 worth of prizes were also given out on the day.