Protests took place outside at least two universities, with tear gas reportedly fired.
US President Donald Trump tweeted support for the "inspiring" protests.
Iran on Saturday admitted downing the jet "unintentionally", three days after the crash that killed 176 people.
Ukraine International Airlines flight PS752, en route to Kyiv, was shot down on Wednesday near Imam Khomeini Airport in Tehran shortly after take-off, and only hours after Iran had fired missiles at two air bases housing US forces in Iraq.
Those attacks were Iran's response to the US killing of senior Iranian commander Qasem Soleimani in a drone strike in Baghdad on 3 January.
Dozens of Iranians and Canadians, as well as nationals from Ukraine, the UK, Afghanistan and Germany died on the plane.
What happened at the protests?
Students gathered outside at least two universities, Sharif and Amir Kabir, reports said, initially to pay respect to the victims. Protests turned angry in the evening.
The semi-official Fars news agency carried a rare report of the unrest, saying up to 1,000 people had chanted slogans against leaders and tore up pictures of Soleimani.
Image copyrightAFPImage captionStudents had gathered outside Amir Kabir university to pay tribute to the victims
The students called for those responsible for the downing the plane, and those they said had covered up the action, to be prosecuted.
Chants included "commander-in-chief resign", referring to Supreme Leader Ali Khamenei, and "death to liars".
Fars said police had "dispersed" the protesters, who were blocking roads. Social media footage appeared to show tear gas being fired.
Social media users also vented anger at the government's actions.
One wrote on Twitter: "I will never forgive the authorities in my country, the people who were on the scene and lying."
The protests were, however, far smaller than the mass demonstrations across Iran in support of Soleimani after he was killed.
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