It was the 19 year old's 9th career victory on the Japan Golf Tour and the Ã‚Â¥30 million has moved him within striking distance of this year's money list leader Kyung tae Kim who finished in a share of 10th this week.
PGA Tour player Ryuji Imada shared third position with Katsumasa Miyamoto and Toru Taniguchi.
Ishikawa shared the third round lead with Hiroyuki Fujita but both would make slow starts.
Ishikawa bogeyed the first hole and Fujita the third but Ishikawa quickly recovered with four birdies before the turn. Ishikawa then added birdies at the 10th and 11th to essentially take control of the event.
A bogey at the 17th came all too late for his chasers and when he birdied the last Ishikawa had won by two over Jones who, as he had with his victory in 2007, eagled the final hole.
Jones earned Ã‚Â¥15 million and moved to sixth on the Japan Golf Tour's 2010 money list with season's earnings of Ã‚Â¥72,359,438.
The Japan Golf Tour will now head south to Miyazaki for this week's Dunlop Phoenix event where defending champion Edoardo Molinari , Australian Robert Allenby and two time winner, Tom Watson, head the international invitees to play against the Japan Golf Tour's elite.
Want video tips delivered straight to your inbox? Subscribe to iseekgolf.com newsletters.