Initial reports suggested the attack was a double bombing, with one explosion taking place inside the supermarket and one outside.
"The first bomb was small and no one was hurt but the second bomb was huge - I don't know yet whether it's a car bomb or not," Captain Preecha Prachumchai of Pattani provincial police said.
The first car bomb in Pattani since August destroyed the front of a Big-C supermarket, scattering debris over a wide area and sending up a column of black smoke.
The attackers initially set off firecrackers as a distraction before triggering the car bomb, said military spokesman Pramote Prom-in.
Pictures posted on social media showed the charred remains of cars and motorcycles, and victims being treated at the scene for injuries.
Two of the 42 wounded were in a critical condition, authorities said.
The bombing was swiftly blamed on Muslim separatists in the predominantly Buddhist country.
A decades-old separatist insurgency in the largely ethnic Malay Muslim provinces of Yala, Pattani and Narathiwat has killed more than 6,500 people since 2004, according to independent monitoring group Deep South Watch.
Attacks in Thailand's deep south have intensified this year.
Last month, the government rejected a conditional offer for peace talks by one of the main insurgent groups, the Barisan Revolusi Nasional, which demanded international mediation or observation.