A new law, passed by 130 votes to 44, will force groups receiving more than 24,000 euros (USD 26,000) annually in overseas funding to register as a "foreign-supported organisation", or risk closure for non-compliance.
The government of populist premier Viktor Orban says the measures are aimed at improving transparency as well as fighting money laundering and terrorism funding.
But the European Commission and the United Nations have condemned the law, saying it could "discriminate against and delegitimise" non-governmental organisations (NGOs).
It "has nothing to do with transparency and everything to do with obstructing and discrediting critical civil society voices," said Amnesty International's European director, John Dalhuisen.
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The organisation denounced the move for resembling legislation introduced in Russia in 2012 requiring foreign NGOs to register as "foreign agents".
The Hungarian law marks a hardening of frontlines in Orban's battle with foreign-funded NGOs, in particular those receiving support from Hungarian-born emigre Soros.
Government-backed billboard and media campaigns have targeted the philanthropist, while a questionnaire sent to households nationwide urged support for the registration of foreign-funded NGOs.
Earlier this month the EU's rights watchdog Venice Commission said the NGO bill was "excessive" despite pursuing "legitimate aims", and urged the government to consult local civil society groups.
It also accused "some state authorities" of staging a "virulent" campaign against NGOs.
Budapest said it took the Venice Commission concerns into account when amending the proposal last week, for example dropping a requirement for the details of all foreign donors to be named on a group's publications.
"NGOs can still be closed down if they fail to comply with the new rules," the HHC's co-chief Marta Pardavi told AFP.
"No consultations took place before the vote, while the general intent to stigmatise also remained," she said.
Today's vote follows the hasty approval of another law in April that threatens to shut the Soros-founded Central European University in Budapest.
The crackdown on the CEU and NGOs sparked a large protest in April in the Hungarian capital.