The Attorney General's Office for Environmental Protection said two other tourists suffered "considerable" injuries when the whale breached and hit the side of the boat on Wednesday.
The office said the boat had been carrying nine tourists on a snorkel tour and quite near shore when the incident occurred. It described the rigid-hulled vessel as "a fragile type with inflatable parts."
Photos showed the open boat - about 25 feet long, with twin outboard motors - apparently undamaged after the collision.
A crew member and a passenger lifted her back onto the vessel and Mexican navy personnel moved the woman to shore.
She was taken to a clinic, where she died during treatment.
Whales surface to breathe, often unexpectedly. Collisions between whales and boats are not unknown in Mexico, where whales come to breed in coastal lagoons in winter. Authorities generally require boats to stay a safe distance away from whales in whale-watching areas and protected reserves, but those rules don't apply in the area around Cabo San Lucas.
