Thank you for the replies. I think I lucked out with the couple's choice in godparents which helped confirm the connection. If they had just chosen family friends as their children's godparents, then I might never have been able to connect the baptism records to the marriage record.
Interestingly, there is another couple named Manuel de Aguiar and Antonia de São Jose who were married in Bretanha about ten years later. I've found many trees online where people have conflated the two couples and mixed up records. It's understandable since, as you say Nelson, different variations of women's names can appear in records (not to mention just plain scribal errors), but you have to be very careful when it comes to connecting one record to another, which is why I'm always extra cautious.