Indigenous warfare as a whole tends to be a little one-sided. While it is true that battles have been fought and won by tribes around the world, in the end the Europeans tended to win. The tribes that the Europeans had the most trouble with were the nomadic tribes, in particular the Lakota in the north and some Amazonians in the south. These tribes lacked any sort of nerve center to attack and destroy and with their nomadic lifestyle typically came a distributed chain of command and supply chain. This made the tribe as a whole less efficient, but allowed it to sustain the loss of a leader or the occupation of territory without the same tactical setbacks that a more structured group would. These advantages were typically not available to tribes that had established towns as towns could be occupied and ruled through force in a way that a mobile group never could be. And yet, the O'Odham effectively fought the Spanish (later the Mexicans) without the same kind of catastrophic losses that faced other sedentary tribes.
The reason for the relative success of the O'Odham is in part due to geography. The productivity of the land was such that any O'Odham towns were small enough and far enough apart to make effective rule by a Spanish official (Alcalde) difficult. This is will documented in the struggles that missionaries had in converting the O'Odham and is probably part of the reason that Father Kino adopted his nomadic pattern of work. The lack of productivity also probably made the O'Odham less important to the Spanish than the more developed and more productive fields farther south. But beyond geography the O'Odham used unique tactics that would be later classified as guerilla.
The O'Odham did not have a standing army or a central government and when the Apaches would attack the defense of the O'Odham would be left to irregulars, people who had other jobs but would also fight when called upon. When the Spanish advanced with military forces the O'Odham innovated on the same tactics. The Spanish would advance into O'Odham territory face raids on their forces without warning but when they went to pursuit they wouldn't find anyone to fight. The O'Odham army would have already dispersed and the fighters would be back in their homes.
Although this strategy did not expel the Spanish or their influence from the O'Odham territory, the O'Odham used war to remind the Spanish that they would not completely bow down.