The court ruled it has no authority to handle the case. Jurisdiction in the matter rests with the Supreme Court's Criminal Division for Holders of Political Positions, it said.
The special cases prosecutors initially filed two lawsuits with the Criminal Court seeking the indictment of the two men, as recommended by DSI investigators.
The action followed Criminal Court rulings on several cases that some protesters were killled and wounded by gunshots fired by soldiers acting on the orders of the Centre of the Resolution of the Emergency Situation (CRES), which was set up by the then-Democrat-led government under Mr Abhisit.
Mr Abhisit was first to acknowledge the charges. Mr Suthep, who has entered the monkhood and is now in Surat Thani, reported to the court later to hear the charges. He donned the saffron robe after the protest by the People's Democratic Reform Committee (PDRC), which he led, against the Yingluck Shinawatra government ended following the May 22 coup.
The cases against Mr Abhisit and Mr Suthep were later merged as one. Mr Abhisit was the first defendant and Mr Suthep the second.
The two were charged with murder and attempted murder under Sections 80, 83, 84 and 288 of the Criminal Code in connection with the military crackdown on the protesting supporters of the United Front for Democracy against Dictatorship (UDD) between April 7 and May 19 2010, which resulted in more than 90 deaths and hundreds of injuries.
Both Mr Abhisit and Mr Suthep denied the charges and submitted a petition to the court arguing that the DSI did not have the power to handle the investigation against them.
The Criminal Court on Thursday said it was true that the two men had declared the state of emergency and ordered soldiers to crackdown on the protesters, and allowed them to use weapons and live ammunition.
But Mr Abhisit and Mr Suthep issued the order while performing the duties of the prime minister and deputy prime minister respectively.
The Criminal Court, therefore, ruled that the case against the two men comes under the jurisdiction of the Supreme Court's Criminal Division for Holders of Political Positions and that it has no authority to handle the case.
Since a petition has also been filed against Mr Abhisit and Mr Suthep with the National Anti-Corruption Commission, which is responsible for handling criminal cases against politicians, the court also ruled that if the NACC finds the petition against them has sufficient grounds, the graft agency is duty-bound to forward the case to the Supreme Court's Criminal Division for Holders of Political Posts for further consideration.