The two monks were slashed in separate but near-simultaneous attacks by assailants riding motorcycles in Yala province early on Saturday as they walked along the street receiving alms, a policeman from Yala station said.
One was slashed across the back of the head and the other in the neck, while a third monk was wounded in the back but was not killed, he said.
Sectarian violence is rare anywhere in Thailand, and the murders of the monks were the first such attacks in the Muslim-dominated south in several years. About 90% of Thailand's 63 million people are Buddhists.
Thailand's south has been rocked by a series of attacks on government targets since early this month leaving six dead, while on Thursday the violence flared anew with the fatal stabbing of a Buddhist monk in Narathiwat.
Police said they feared the unusual attack was linked to the recent unrest, which has previously targeted security rather than religious figures.
Prime Minister Thaksin Shinawatra blamed Saturday's attacks directly on separatists whom he said were trying to provoke religious conflict.
"The public must remain patient and not be swayed by the some 200 separatists who are trying to win support from the public. Thailand's soil cannot be divided"
Thai prime minister
"These were continuing attacks by a group of people who are trying to create conflict between Buddhists and Muslims," Thaksin said during his weekly radio address prior to the confirmation of the deaths.
"The public must remain patient and not be swayed by the some 200 separatists who are trying to win support from the public.... Thailand's soil cannot be divided," he said.
Thaksin also criticised Muslim Thais for failing to cooperate with the government. Five arrests have been made in connection to the earlier attacks but no charges have been laid.
"Muslim Thais in the three provinces still do not want to give information to officials," he said.
Meanwhile, a policeman was fatally shot in the head while riding his motorcycle home from work at Kapho district police station in neighbouring Pattani province at 9:30 pm (1430 GMT) Friday, police said.
The latest spate of attacks in the region, home to a long-running but now considerably weakened separatist movement,
began on 4 January with a daring raid on an army depot in Narathiwat province that killed four soldiers and simultaneous attacks on 18 schools and two police checkpoints.
Two bomb squad officers were killed the next day as they attempted to defuse a bomb in Pattani and shortly afterwards a shooting spree at a Yala police station left two policemen wounded.
Muslim students walk past a torched
school in Narathiwat province
In response to the attacks, the government introduced martial law in several districts in the three affected provinces, which both Thaksin and Deputy Prime Minister Chavalit Yongchaiyudh said would remain in force despite some requests by Muslim leaders to end it.
Chavalit admitted the situation in Thailand's three southernmost provinces had reached a crisis.
Buddhists are a minority in the southern provinces, but tend to be wealthier than the majority ethnic Malay Muslims there who regard ethnic Thais as outsiders.
Buddhists hold most of the top civil service and police posts in the area, which can put them at odds with the populace.