Matsumoto, a member of Victoria Golf Club, finished with rounds of 71-76-76-77 (+8) to defeat Queenslander and Australian Amateur runner up Karis Davidson by one.
The 14 year-old, who was born in Japan, was thrilled with the win.
"It's great - I was really nervous in the morning (third) round and again this afternoon," Matsumoto said.
"I've been practising so hard for this - I was hoping for at least a top 3 finish and after my first round, it gave me a lot of confidence."
Matsumoto competed at this year's ISPS HANDA Women's Australian Open at Victoria Golf Club via an invitation and, through today's win, gains an exemption into the 2015 championship.
"It means so much. I only found out yesterday that there was exemption. I learnt so much in February - mainly you have to keep playing your game. You can have one bad hole but you can't give up," Matsumoto added.
Queensland's Rebecca Kay finished in third place at 11-over par.
The Girls' Interstate Teams' Matches will be played from 13-15 April at the same venue with New South Wales, Queensland, South Australia, Western Australia and Victoria contesting the event.
h3. Australian Boys' Amateur Championship - The Heritage Golf and Country Club - Final Round
Victorian Ryan Ruffels capped his performance with a 72nd hole birdie to win the Australian Boys' Amateur Championship by three strokes on the St.John Course at The Heritage Golf and Country Club.
Ruffels fired rounds of 70-69-68-70 to finish at 11-under par on a rain-soaked course, three clear of New South Welshman Blake Windred who closed with a 4-under par 68. Victorian Brett Coletta finished third, three strokes further back.
"Blake and Brett are both really good players and better than that, they're really good guys. We had a lot of fun out there today," Ruffels said.
"For me the first two rounds, I just kept the ball in front of me. The fairways are nice and wide so you've just got to be able to hit the fairways and with the greens this soft, you're able to get aggressive with the second shot. I was able to hit it close enough to take a bit of stress off the putting and ended up playing pretty stress-free golf for most the four rounds which was great."
Ruffels continued on his recent good form which included victory at the recent Riversdale Cup in Melbourne.
"I think there were four or five guys that came in this week as pretty strong favourites and there are a lot guys in state squads that are really good. To be able to beat those guys this week - I knew I had the ability to win it - but it's just about doing it and I'm very relieved," Ruffels added.
The 15 year-old's exemption into the Emirates Australian Open in November will be his second consecutive appearance.
"I had so much fun playing at the Aussie Open last year, got to play with some really cool guys and obviously having a good tournament as well. It's good to have secured that spot," Ruffels said.
The Boys' Interstate Teams Matches will be played from 13-16 April will all Australian states and territories represented.