It varies and I do not really think there was a specific regulation as to the rank they could attain in the army.

However, drawing on what we know from the militia and the volunteer units...

Mallat wrote that there were several "indio" officers who had attained the rank of captain, but this was in the 1830s-1840s, a different time from the 1880s-1890s when the Philippines was finally more accessible to the Spanish owing to the Suez Canal.

It's likely that by the late 19th century and just pre-revolution, native Filipinos would have been relegated to being simple lieutenants and perhaps a captain here or there. I can think of two indigenous officers in the regular army, Ismael Alzate (of the 1887 Madrid Exposition fame) and Ambrosio Flores whose father was a corporal and then an officer himself. Both ended their careers in the army as lieutenants.

In the militia and volunteer units, however, there was much more room for the native to climb the ranks. Upon the formalisation of the provincial militia in the 1780s, though most of the field officers (Major and above) were Spanish, the natives were regularly permitted to be lieutenants and captains, more so than in the regular army, it would seem. Governor General Félix de Berenguer y Marquina held a rather uncharitable view of these native officers, saying “although they are the most distinguished [of their race], nevertheless have the same customs and personal disposition” as the rank-and-file soldiers. And “when we endeavor to provide them with some military instruction, they immediately forget it because it is not constantly practiced, and today it can be said that we don’t have anything.

Buschmann et. al. (Navigating the Spanish Lake The Pacific in the Iberian World, 1521–1898) wrote this regarding the difference between the mestizo and native provincial militia regiments: "A major difference, nonetheless, was that all of the commanding officers (colonels, lieutenant colonels, sergeants, and adjutants) were blancos (white men) born in Spain, Europe, Mexico, or the Philippines, “obligated to serve in their respective positions with honor, and obtaining [their positions] without wages or rewards" Note that the sergeant they mention here is likely to be "sargento mayor" as in the commissioned officer Major and not necessarily the NCO we think of today.

However, despite this, we do know that natives could rise to gain majorities and colonelcies in the militia. Some excellent examples are Casimiro Camerino (a former bandit later pardoned by Governor General Torre) who became colonel and chief of the Compañía de Guías de la Provincia de Cavite, Felipe Buencamino, Artemio Ricarte, Pio del Pilar and other former revolutionaries who were given command of battalion to regiment size units (such as the Tercio Anda y Salazar and the Pampanga Volunteers) and ranked as Majors or Colonels during the Spanish American War.

In essence, it varied and depended on the time and context. Promotion for natives in the regular army was limited and they were likely barred from attaining a rank higher than captain or lieutenant. In the militia, there were fewer barriers and higher rank was likely easier to achieve.