The attackers wanted the vehicle for its tyres and shot the tourists when they resisted, Baja California state prosecutor Maria Andrade suggested.
Their bodies were found in a 4m (15ft) deep well about 6km (4 miles) from the site of the attack in the town of Santo Tomás on Friday.
Abandoned tents, a burnt white pickup truck and a phone linked to the missing surfers were found nearby.
A fourth body was found in the well, but had been there longer and was unconnected to the case, officials said.
Two men and a woman have been detained on suspicion of direct or indirect involvement in the attack. One man with a previous criminal record has been charged with "forced disappearance".
Earlier, the FBI said it was looking into the case and was in touch with international partners.
Baja California is one of Mexico’s most violent states, as local drug gangs fight turf wars.
In 2023, it had the country's second highest murder rate, after the state of Guanajuato, according to official figures.
National Defence Secretary Luis Cresencio Sandoval said earlier this year that 85-90% of murders committed in Baja California were linked to drug trafficking and organised crime.
But the Ensenada area, about 120km (75 miles) south of the US-Mexico border and known for its surfing conditions, is considered safer and has long attracted tourists from California.
Iwantmy3rdpartyapp on May 6th, 2024 at 10:29 UTC »
What the fuck?
fluffyfurnado1 on May 6th, 2024 at 10:17 UTC »
The two Aussies were brothers. It’s unimaginable to have one son die, but two is just the worst pain I can ever think of.
Cerda_Sunyer on May 6th, 2024 at 10:17 UTC »
What tyres were on that pickup that they would be killed for?