In a press conference Sunday, Syria's information minister Omran al-Zoubi said that the attack was incompatible with the government's values.
"[Syria] did not commit and would never commit such an act because our values would not allow that," he said, according to BBC.
Turkish authorities said they had detained nine people in connection with the bombings.
All of the detained are citizens of Turkey that authorities believe were in contact with the Syrian government.
Turkey's Deputy Prime Minister Besir Atalay said it was clear Syria was behind the attack.
"The investigation into the perpetrators is for the most part complete. It has been determined that the organization and its members who carried out the attack were in contact with pro-Syrian regime Al Muhabarat (Syrian Intelligence Services) organization in Syria," he said, according to CNN.
"The organization is identified and for the most part the persons involved are identified. "
In an interview on Turkish television, the interior minister, Muammer Guler said there was no doubt Syria was behind the attack.
“The incident was carried out by those who have been closely linked with pro-regime groups in Syria,” Guler said, according to the Associated Press.
“There is no merit in spelling out the names, we know them all."
Meanwhile, hundreds marched in the streets of Antakya Sunday in protest of the Turkish government's support of the Syrian opposition. They carried anti-government banners and chanted as police stood by with riot gear, reported GlobalPost senior correspondent Tracey Shelton.
Two car bombs were detonated on Saturday afternoon in the southen Turkish town of Reyhanli.
The bombs killed 46 people as of Sunday afternoon and critically injured 29.
It is believed that 155 were injured in the attack.
The bombs exploded in front of municipal government buildings and a post office.
Reyhanli, next to the Syrian border, is believed to have over 300,000 Syrian refugees who have fled the violent conflict that began in March 2011.
Despite the protests, some Turkish people remain skeptical that Assad was behind the attacks.
"You must look carefully at the timing," Antakya resident Kenan Sakar told GlobalPost, referring to recent efforts to arrange talks between the FSA and the Syrian regime. "The global media must ask this: Reyhanli and the Idlib border are under the control of the FSA, so how could Assad bomb there? Also, for example, if they could access this area, why would the Syrian government not bomb the headquarter of the FSA?"
"If you remember before some days ago, the NATO general secretary said, 'We are ready to protect Turkey from Syrian attacks,'" Sakar added.
Dr. Ubada Alabrash, a doctor with Syrian/Arabic origins working in Reyhanli Hospital, told GlobalPost the scene on Saturday was chaotic as patients from the blast arrived.
"Emotions were high. People were terrified," he said. "All the Syrian people stayed in their homes. It was not a good time to be in the face of the Turkish people."
"It’s not that the Turkish people are blaming the Syrians," he added, "but it is an emotional time for them."