The two Muslim civilians were killed as they left a tea shop in Narathiwat province when four assailants got out of their pickup truck and fired dozens of shots from assault rifles, police Lieutenant Vorapong Klomsakun said.
In Yala province, a roadside bomb wounded three border patrol policemen who were in a van on patrol duty.
Another bomb, hidden beneath a motorcycle, exploded in front of a school in Narathiwat, wounding one policeman.
The bomb was triggered by a mobile phone, police said.
Meanwhile, three men were arrested in connection with a 30-minute gun battle on Tuesday night in Pattani province, in which three policemen and two suspected fighters were killed, army spokesman Akara Thiprote said.
In a separate raid at a mosque in Narathiwat, the authorities found a cache of camouflage and military-style uniforms, two-way radios, ammunition and maps of government offices.
More than 2,000 people have died since January 2004 in Thailand's southern provinces of Yala, Narathiwat and Pattani as a result of the separatist uprising.
Government measures to quell the violence have failed to gain any noticeable ground.