Just before the execution, Coatl confesses to Father Bartolomé that he killed de Silva, but before Pedro can be freed, Catana stabs him with a knife to spare him the degradation of being hanged.
He killed de Silva. This is what Coatl confesses to Father Bartolomé just before the execution. Catana stabs him with a knife to spare him the degradation of being hanged. Pedro can be freed.