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.