Though the vote was largely symbolic, as she had already lost her post, it also carries a five-year ban from politics.
The news came hours after the attorney General's office announced that Yingluck, who was removed from office in May last year days before the military swept to power in a coup, will face criminal charges over the affair.
If found guilty, she could face up to 10 years in prison.
The rice subsidy program, introduced in 2011, pledged to pay farmers well above the market rate for their crop. But critics said it wasted large amounts of public funds trying to please rural voters, hurting exports and leaving the government with large stockpiles of rice it couldn't sell without losing money.
She was eventually put under investigation by Thailand's National Anti-Corruption Commission (NACC).
In an address to the NLA Thursday, Yingluck denied any wrongdoing and questioned whether the impeachment vote was valid.
"The NACC's legitimacy in sending the impeachment case for the NLA's consideration is questionable since the Constitution of 2007 has been revoked ... with the coup d'etat on May 22, 2014," she said.
"I am no longer prime minister since the constitutional court has already removed me, thus there is essentially no 'position' to impeach me from.
"The legal grounds claimed by the NACC were also invalid, as the target of impeaching me is to ban me from holding any political positions for five years, which is a clear violation of my fundamental rights and liberties."
But the Bangkok Post
reported Friday that many NLA members were unconvinced and found she was unable to clear up the accusations against her. They also backed the NACC evidence against her.
'I am sad for the rice farmers'
In a statement translated into English by her office, Yingluck said she would "continue to fight to prove my innocence to the very end, no matter what the outcome will be."
She said the rice subsidy scheme was "beneficial for the farmers and the country" and that claims it lost money were wrong and motivated by political bias against her.
"I am not sad because I am the victim of this entire ordeal, but I am sad for the rice farmers and all of the disadvantaged Thai citizens whose lives will return to the vicious cycle of being poor, debt ridden, and being taken advantage of, and most important of all, being denied of their basic democratic rights under the rule of law," she said.
Violation of constitution
Two weeks before the military coup last May, a Thai court ordered Yingluck's removal, finding her guilty of violating the country's constitution in her reassignment of a senior security official in 2011. That official was replaced by the then-national police chief, whose role in turn was given to Priewpan Damapong.
Damapong is the brother of the ex-wife of Thaksin Shinawatra, Yingluck's brother, who was overthrown as Prime Minister in a military coup in 2006. Thaksin is living in self-imposed exile to avoid a corruption conviction.