Without drastically altering the far past to the point that the culture in the Malay archipelago (and probably Asia overall) is so different as to not really be anything like OTL's it's not really possible.
Let's look at a few points;
-Chinese influence on Japan goes back two thousand years.
-Japan's history as a sociopolitical entity goes back just as far, with the first Japonic state being recorded to exist in about 300 BCE and modern Japan (as opposed to Japonic or early Japanese states) having come into existence in the 9th century CE.
-The earliest sophisticated empire in Malaya, Srivijaya came into existence in the 7th century CE and at it's height only controlled the Malay peninsula and parts of Java and Sumatra and was very focused on that region.
-By the time that Japan began to trade with the region it was already a sophisticated state with an established society and large (for the time) population, and that trade was not exactly robust or always direct.
-The Philippines was until the Spanish conquest comprised of many different small kingdoms comprising many different societies and religions and had no overarching society that could influence Japan, indeed if anything closer relations between Japan and the Philippines at the time would lead to the Philippines becoming Japanized rather than Japan becoming Malay-influenced.