/u/EnclavedMicrostate, good question.

While Portugues-Spanish rivalry in colonial matters was already well-established, there were key mitigating factors. The first factor were the Tordesillas and Zaragoza treaties, which theoretically divided trading and colonization rights between the two nations. In the Atlantic, it gave most of Africa to Portugal and most of the Americas to Spain, with fairly clear lines of navigation. In the Pacific, things were quite a bit murkier, in particular because there was no comprehensive measurement of longitude until Philip II of Spain commissioned a project in 1577-88 to perform longitudal measurements of his vast empire. Regardless, the communication lines in the Pacific were extensions of those in the Atlantic. That meant that to reach Manila, the Spanish had to go through their Americas holdings first. To reach Macao, the Portuguese had to sail around Africa and through the Indian Ocean. The second factor was the conditions of the personal union of Portugal and Spain under Philip II, promulgated in the Cortes of Tomar in 1580, which states that the two empires shall remain separate as they had been.

Pragmatically, the farthest outposts in the far east were operating with significant independence from their respective monarchs (or, equivalently, with very little control therefrom). Portuguese Macao was ruled from Malacca, which in turn was ruled from the Viceroyalty of Goa. Spanish Manila was ruled from the Viceroyalty of New Spain in Mexico. And further, they had many common adversaries. As a result, even as the Portuguese restoration led Macao to declare for John IV Braganza, a degree of accommodation remained. This is not to say there was no conflict, however they were limited to minor ones. When Portuguese restoration was declared, news reached Goa and Macao much faster than it did Manila. Both Goa and Macao declared for John IV immediately. The Portuguese representative in Manila convinced the un-informed Spanish governor to send a small force to assist in securing Macao for Philip II. Upon arriving in Macao, this un-informed small force was forced to surrender to the Portuguese. This was the only significant premeditated act of hostility I am aware of.

For more references, see C.R. Boxer's publications on the Portuguese Seaborne Empire.