Thai Kiradech Aphibarnrat topped the two-day event at the Amata Spring Country Club in Thailand with a flawless nine-under-par 63 for a 131 13-under total, while China's Wu Ashun clinched the other ticket to Muirfield after two 68s left him on eight-under.
Matsuyama agonisingly missed out on an Open place last year when he dropped six shots in the final three holes.
The nerves returned this year as he wobbled slightly by going bogey, double bogey on the 16th and 17th holes before a birdie on 18 saw him home in second, three shots ahead of a group of four players including Javi Colomo of Spain.
The rollercoaster three-under-par 69 means he can look forward to a third major appearance after playing in the Masters in 2011 and 2012.
"This is my first appearance at the Open and I can't wait for it," said the 21-year-old, who won the 2010 Asian Amateur Championship.
"I gained a lot of experience when I played in the Masters and it improved my game and maturity. I'm sure I'll become even better after playing in the Open."
Kiradech, who finished third in the Myanmar Open on Sunday after leading the Asian Tour season-opener at the halfway mark, set the course alight with a flawless 63, reeling off six of his nine birdies on the front nine.
"I'm glad I achieved my first dream in golf which is to play in a Major championship," said Kiradech, nicknamed "Asia's John Daly" for his grip-it-and-rip-it style.
"I want to do my best at the Open. It will be the biggest challenge and event in my life," the 23-year-old.
Twice Asian Tour winner Maruyama signed off with eight birdies in a 65 to qualify for his first ever Major championship in joint third with Wu, who became the second Chinese player after Liang Wen-chong to seal a place in golf's oldest Major.
Overnight joint leader Siddikur saw his dreams of being the first Bangladeshi to play at the Open dashed after sending his tee shot into the water on the par three 17 for a double bogey. His second round one-over-par 73 leaving him tied ninth on five-under.
Chinese prodigy Guan Tianlang, who at 14 will become the youngest player to compete at the Masters in April, totalled three-over after rounds of 73 and 74.