Short answer. Yes, but not exclusively. Article 1684 provides that land tenancy on shares is governed by special laws, the stipulations of the parties, the provisions on partnership, and the customs of the place. So the Civil Code's partnership rules are one of four sources this kind of farming arrangement draws on, not the only one.
What the law says
Land tenancy on shares shall be governed by special laws, the stipulations of the parties, the provisions on partnership and by the customs of the place.
Civil Code, Article 1684 — Land Tenancy on Shares. Read the full provision →
The four sources Article 1684 names
Article 1684 states, in a single sentence, that land tenancy on shares shall be governed by special laws, the stipulations of the parties, the provisions on partnership and by the customs of the place. So the article does not treat share tenancy as governed by any one body of law alone; it names four distinct sources — special laws, the parties' own stipulations, the Civil Code's partnership provisions, and local custom — that together govern this kind of arrangement.
Where partnership rules fit in the hierarchy
The partnership rules are named explicitly as one of the four, which directly answers your question: yes, the Civil Code's provisions on partnership do apply to a share-tenancy farming arrangement, at least as one of several governing sources the article recognizes. That reflects the underlying nature of a sharing arrangement over land — dividing the produce or proceeds between landowner and tenant resembles, in some respects, the kind of shared undertaking partnership law addresses.
Special laws come first
Special laws are listed first among the four sources, and land tenancy has historically been the subject of specific agrarian and tenancy legislation in the Philippines. Where such special laws address a particular aspect of a share-tenancy arrangement, that legislation is the source Article 1684 names first, ahead of the general partnership provisions of the Civil Code, though the article's text does not itself spell out a strict order of priority among the four sources it lists.
Party stipulations and local custom
The remaining two sources are the stipulations the parties themselves have agreed to, and the customs of the place where the tenancy arrangement exists. Both give room for the specific terms landowner and tenant actually agreed on, and for locally established practice, to shape how the arrangement works, alongside whatever special laws and partnership provisions also apply to the same relationship.
What this means practically
Practically, this means a share-tenancy dispute cannot be resolved by looking at partnership law alone, nor by ignoring it entirely. Article 1684 treats the Civil Code's partnership provisions as one legitimate source among four, to be read together with any applicable special legislation, whatever the parties themselves agreed to, and the customs prevailing in the place where the tenancy exists.