Demonstrators set upon the heir to the throne's limousine as it drove through London's West End shopping and entertainment hub. Protesters who had been running amok and smashing shop windows kicked and threw paint at the car, which sped off.
Charles' office, Clarence House, confirmed the attack but said "their royal highnesses are unharmed."
Police said it was unclear whether the royals had been deliberately targeted, or were simply in the wrong place at the wrong time.
The couple arrived looking composed at the London Palladium theater, where they were attending a Royal Variety Performance. Their Rolls Royce limousine was left with a badly cracked rear window and was spattered with paint.
Protesters erupted in anger after legislators in the House of Commons approved a plan to triple university fees to £9,000 a year.
As thousands of students were corralled by police near Parliament, some strummed guitars and sang Beatles songs - but others hurled chunks of paving stones at police and smashed windows in a government building.
Another group ran riot through the busy shopping streets of London's West End, smashing store windows and setting fire to a giant Christmas tree in Trafalgar Square.
Police condemned the "wanton vandalism." They said 38 protesters and 10 officers had been injured, while 15 people were arrested.
The violence overshadowed the tuition vote, a crucial test for governing Conservative-Liberal Democrat coalition, and for the government's austerity plans to reduce Britain's budget deficit.
It was approved 323-302 in the House of Commons, a close vote given the government's 84-seat majority.
Many in the thousands-strong crowd booed and chanted "shame" when they heard the result of the vote, and pressed against metal barriers and lines of riot police penning them in.
Earlier small groups of protesters threw flares, billiard balls and paint bombs, and officers, some on horses, rushed to reinforce the security cordon.
The scuffles broke out after students marched through central London and converged on Parliament Square, waving placards and chanting "education is not for sale" to cap weeks of nationwide protests aimed at pressuring lawmakers to reverse course.
The vote put Deputy Prime Minister Nick Clegg and his Liberal Democrat party in an awkward spot. Liberal Democrats signed a pre-election pledge to oppose any such tuition hike, and reserved the right to abstain in the vote even though they are part of the governing coalition proposing the change.
Those protesting in central London were particularly incensed by the broken pledge from Clegg's party.
"I'm here because the Liberal Democrats broke their promise," said 19-year-old Kings College student Shivan David from London's Trafalgar Square. "I don't think education should be free but I do think that tripling fees doesn't make any sense. We are paying more for less."
Inside the House of Commons and to the jeers from the opposition lawmakers, Liberal Democrat Business Secretary Vince Cable insisted that the new tuition plans were "progressive" as a heated debate over the proposal began.
Many in his party disagreed, and 21 Liberal Democrat lawmakers - more than a third of the total - voted against the fee hike. Another eight, including at least one government minister, abstained.
Demonstrator John Dawson, 16, admitted that it might be too late to change lawmakers' minds but said protesters must keep up the fight.
"The fact that so many students came out to protest today shows that, even after the vote, they will still do whatever they can to avoid paying this much for higher education," he said.
Experts warned that fallout from the policy could pose a greater risk after the vote.
"The real danger for the government is not that they won't pass it through, but that it will be a policy fiasco," said Patrick Dunleavy, a political science professor at the London School of Economics. "By picking this fight with the student body ... the government seems to have gotten itself into choppy water."
All of this has made Clegg one of the least popular politicians on university campuses. Protesters chanting "Nick Clegg, shame on you for turning blue" underscored the sense of betrayal.
Clegg defended the proposals, saying the plans represent the "best possible choice" at a time of economic uncertainty.
"In the circumstances in which we face, where there isn't very much money around, where many millions of other people are being asked to make sacrifices, where many young people in the future want to go to university, we have to find the solution for all of that," Clegg told the BBC.
Cameron's government describes the move as a painful necessity to deal with a record budget deficit and a sputtering economy. To balance its books, the U.K. passed a four-year package of spending cuts worth 81 billion pounds, which will eliminate hundreds of thousands of public sector jobs and cut or curtail hundreds of government programs.
The government proposed raising the maximum university tuition fees in England from £3,000 a year to £9,000. Students reacted with mass protests that have been marred by violence and have paralyzed some campuses.
In response, the government modified its plan by raising the income level at which graduates must start repaying student loans and by making more part-time students eligible for loans.
Students have said the concessions are not enough to lessen the blow of higher fees. They say that under the proposal, piles of debt will plague graduates and make a well-rounded education unattainable for many.
The controversy has highlighted regional educational differences in the United Kingdom.
The Welsh regional government has pledged to subsidise the higher fees for any student from Wales who enrolls at an English university. Student fees in Scotland are just £1820 per year, sparking fears of a future stampede of bargain-hunting students from England. Northern Ireland's fees are capped at £3290 a year.
