With a four-shot advantage after two rounds, the 54-year-old Thaworn shot a two-under-par 70 in the final round at Eastwood Country Club for a total of 203, two strokes ahead of Prayad.
Thaworn took home ¥10 million (B2.83mn) while Prayad, 55, received ¥4.75mn (B1.35mn) after making a 68 in the final round.
This was the first tournament on the tour for both Thaworn and Prayad in almost two years due to the COVID-19 pandemic.
They went to Japan last month and entered a 14-day quarantine. They then took part in the Asia Pacific Diamond Cup on the regular Japan Golf Tour where both missed the cut.
The duo have been among the top players on the Japan Senior Golf Tour over the past few years.
They have claimed a combined 19 titles on the over-50 circuit with Prayad winning 15.
Prayad won the Order of Merit title from 2016-2018, while Thaworn was crowned money champion in 2019.
They will next play at the Starts Senior Golf Tournament in Ibaraki from June 11-13.
Thongchai takes lead
Thailand’s Thongchai Jaidee took a one-shot lead after hitting a 65 in the first round of the Principal Charity Classic in Des Moines, Iowa, on Friday.
Dicky Pride and Doug Barron sit tied second one shot back after matching 66s.
Thongchai, 51, was making his fifth start on the PGA Tour Champions (senior tour) and first appearance at Wakonda Club.
“I love the golf course. It’s very challenging. It’s not very long, you have to keep the ball in play and putt well,” he said.