A leading Greens MEP branded the move the "latest blow" against the rule of law in Turkey which "again drives home" that it is "wrong" for EU to rely on Turkey to solve the refugee crisis.
Pro-Kurdish lawmakers say the vote will expel opposition members from Parliament.
The measure is seen as targeting the pro-Kurdish Peoples' Democratic Party (HDP) as well as the main opposition Republican People's Party (CHP).
Turkey has led an offensive against the outlawed Kurdistan Workers' Party (PKK), accused of being a terror group.
A ceasefire ended weeks after elections in June 2015. The renewed conflict has claimed hundreds of lives on both sides, particularly in the south east.
Turkish President Recep Tayyip Erdogan accuses the HDP of being the PKK's political arm and has called for pro-Kurdish MPs to face terrorism charges. The vote could be a first step towards making that happen.
However, Greens/EFA co-Chair Rebecca Harms has roundly condemned the move, saying, "Erdogan is redesigning Turkey's politics and state with the goal of strengthening presidential power. Today's decision deals Turkey's parliamentary opposition a decisive blow, as almost all of its deputies will be open to legal procedures and consequently the loss of their seats.
"This undemocratic decision against the HDP opposition party, which is supported by the Kurdish minority but also progressive liberal voters, is a further escalation of the situation in Turkey."
The German MEP added, "The Erdogan regime is taking the country further and further from the basic tenets of democracy and the rule of law. Clearly, the EU must attempt to work with Turkey but this cannot be solely determined through the prism of the refugee crisis."
Harms said, "By stripping a large group of MPs of their immunity, President Erdogan is trying to 'correct' the electoral outcome in his favour. Leaving the opposition open to spurious legal challenges will both weaken it and remove a crucial critical voice from the Turkish Parliament."
She believes Erdogan's aim is "clearly" to secure the necessary parliamentary majority to allow him to change the constitution to his ends and to move towards an even more authoritarian presidential system.
Harms said, "This law is targeted primarily at the HDP opposition party, which gained support from both the Kurdish electorate but also progressive liberal voters in the election."
Its Chair, she notes, has fought for a political solution to the conflict between the government in Ankara and the Kurdish minority, "whereas President Erdogan has refused to engage in the peace process."
She believes that stripping many HDP deputies of their immunity could exacerbate the conflict.
"While the Greens have consistently supported progressing negotiations with Turkey and visa liberalisation for Turkish citizens, it is clear that the continuing slide away from democratic norms should lead the EU to critically assess if the basic conditions for visa liberalisation exist."
She said, "Erdogan's latest blow against the rule of law again drives home that it is wrong for EU to rely on Turkey to solve the refugee crisis."
Turkey was also discussed at the just-concluded European Green Party's 24th council in the Dutch city of Utrecht. It attracted 300 delegates from 30 countries.
Afterwards, the joint chairs of the European Green Party, former MEP Monica Frassoni and German MEP Reinhard Bütikofer, said, "We held talks on migration and the first priority for us is to win the argument that member states can and should accept to take in more refugees and properly organise their distribution among them."
In a reference to the EU-Turkey deal that sees an easing of visa rules for Turkish people visiting Europe in return for Turkey's help in tacking the refugee crisis, it went on, "The necessary agreements to support neighbouring countries like Turkey in hosting refugees should not be exclusively finalized in order to keep our frontiers closed."