"This is my dream. Thank you Japan for giving it to me," an ecstatic Bea Rose Santiago said at the event, held late Tuesday in Tokyo.
"I'm going to use my crown and my title to help the victims" of Super Typhoon Haiyan, which raked the Philippines last month, leaving nearly 8,000 people dead or missing.
"So this is actually for my province, and this is for the Philippines."
Santiago was selected from among 67 candidates representing countries and regions of the world.
In a break with pageant custom, she was crowned by Spain's 2008 Miss International and not by her immediate predecessor, who stayed away from the glitzy show.
"I really wanted to meet her," the new beauty queen said. "It was very unfortunate because I really wanted to meet last year's winner also."
Outgoing title-holder Japanese Ikumi Yoshimatsu told foreign journalists this week in Tokyo that she had been asked by organisers to stay away from the final.
Yoshimatsu said since winning she has faced a running battle to maintain her independence from the management agencies that form the backbone of Japan's entertainment industry.
She said a senior executive at one agency had been in touch with her on many occasions. After she had repeatedly rebuffed him, he telephoned the main sponsor of the Miss International competition, she said.
As a result, the Miss International office in Tokyo began "instructing me, to 'play sick,' 'keep quiet' and not to attend the world final pageant here in Tokyo... to pass on my crown to my successor," she said.
The organiser of the beauty pageant, Tokyo-based International Culture Association, did not return calls made by AFP.
A local tabloid magazine has reported the executive of the management agency denying he was carrying out any campaign of harassment, saying that he was involved in a separate dispute with Yoshimatsu's agent over money.