Well, you need Japan to have an interest in the Philippines.
The first manifestations of territorial imperialism were directed at those areas that had a tradional link with Japan, and/or were largely inhabited by Japanese. In the 1860's and 1870's, attention was thus focused on the Ryukyu islands, the Kuriles, the Bonins, and Sakhalin.
Once matters were mostly settled there, the next areas of focus were on the closer areas such as China and Korea, which were both important and had long-standing feuds or relations with Japan. Only after Japan has achieved its goals here, or at least hit what it considers to be the limit of what is achievable, is it likely that Japan would look out further, for instance towards the Philippines.
Now, there are a few interesting facts:
First, Iyeyasu, before his turning strictly against Christianity, encouraged Japanese merchants to go to the Philippines, Annam, Siam, china and even India, to open up trade routes. During his later years, and during the reigns of Hidetada and Iyemitsu, of course, this was abandoned and Japan became isolationist.
Some earlier Japanese reformists wanted to export Japan's newfound "better way" to other "backwards" countries (preferably peacefully, but with a bit of strong-arming if necessary). In 1869, for instance, after Korea had resisted gentler persuasion to modernize according to Japanese ideals, Kido Takayoshi proposed to bring "our superior national policies to that land" by armed force, believing that this "rationale will be universally accepted".
Edit: removed the sentence about Korea supposedly having been a tributary state. That may have been relevant in the 1500's, but not in the 19th or 20th century...
Finally, while China's population had nearly doubled during the 18th century, while Japan's had remained fairly stable. When, about 1900, Japan's population had grown large enough, emigration principally went to Hawaii and the U.S. West Coast.
Now, it looks to me like we need Japan to have a reason to be unusually interested in the Philippines so that it will make intrusion there a priority before 1898. Otherwise it will focus on closer areas exclusively.
What if, during Iyeyasu's day, a large and thriving Japanese merchant community was established there, and some contact maintained during Japan's isolationist years? With many Japanese living there, Japan is likely to take a renewed interest in the Philippines during those early decades of modernization (1860's through 1870's). It might seem a natural spot for emigration once Japan's population grows (and it would help if population growth accelerated a bit earlier to stimulate renewed emigration to those islands). With the conflict that was endemic there under Spanish rule, it might seem like a good place to showcase Japan's "superior national policies" once Japan developed the military strength to support such an effort at a distance from home.
If Japan developed a bit more modern naval strength in the 1880's, perhaps Japan, anticipating the Spanish-American War's outbreak, positions itself to rapidly jump on the Philippines with an eye to "establishing order" and protecting her people there from potential violence. This will cause a confrontation with the U.S., but since America was divided over the notion of imperial-style expansion in distant regions anyway, this could be managed. The European imperial powers can perhaps be bought off with various concessions, especially if Japan establishes her initial role as Protector-Protectorate instead of outright annexation. What the Europeans really feared at this point was expansion of other European nations' power; at the moment Japan still looks "manageable"; her taking the Philippines might seem more desirable than the prospect of some other European power establishing itself there.
The POD, then, would be a large colony of Japanese being established in the Philippines during Iyeyasu's day, with the necessity of maintaining contact with it reducing the worst effects of isolationism. Japan keeps up a bit better with modern ways pending a full modernizing revolution in the mid 1800's. By not starting from quite so far behind, she develops her ability to project power a bit faster, and is both interested in, and at least minimally capable of, intervening in the Philippines when a weakened Spain is distracted by its conflict with the U.S.
The above isn't great, but it's the best I can come up with at this point.