During a late-night session, a Yerevan court granted a motion by the Armenian special investigation service for the 63-year-old to be held in pre-trial detention, his lawyer Aram Orbelyan told journalists.
Kocharyan has denounced the charges as "false and politically motivated."
"I will go to prison and will fight to the end...I am confident that ultimately I will win because the criminal case is completely falsified," he told Yerkir Media television network earlier.
He could face up to 15 years behind bars if found guilty of tipping a 2008 vote in favour of his political ally Serzh Sarkisian, in what investigators said earlier amounted to a coup.
Armenian opposition leader's bid for PM faces parliament vote
Supporters of the defeated opposition candidate Levon Ter-Petrosyan came out to protest after he denounced the vote as fraudulent.
Tensions then erupted into violent clashes between riot police and Ter-Petrosyan's supporters, in which eight protesters and two officers were killed.
Pashinyan was arrested in 2009 for organising the protests and sentenced to seven years in prison, but was released as part of an amnesty in 2011.
Sarkisian led the South Caucasus nation until April this year, when he was forced to resign because of mass protests against his rule.
Pashinyan--who led the protests--became Sarkisian's successor in May and launched a sweeping, anti-corruption crackdown on former elites.
A pro-Russian politician, Kocharyan served as Armenia's second post-Soviet president from 1998 to 2008.
His presidency saw the bloodiest event in Armenia's post-Soviet political history--the militant attack on the Armenian parliament in 1999.
Opposition parties have accused Kocharyan of organising the attack in which five gunmen killed his political foes, Prime Minister Vazgen Sargsyan and parliament speaker Karen Demirchyan.
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