Gardai removed four people as Mr Kenny delivered a speech at the launch of the UCD Centre and Sports Complex.
The Taoiseach was not hit by the eggs.
Members of Free Education for Everyone (FEE) and Socialist Workers Student Society said students threw eggs to show their opposition to his invitation given speculation that university fees will be increased in the looming budget.
A UCD spokesman said three students had been identified and would be sanctioned under the university's code of conduct.
"There was a protest at the new sports centre," the spokesman said.
"Just before Mr Kenny got up to speak, there was a bit of a protest and two eggs were thrown at the podium he was standing on. Neither of the eggs hit him."
The spokesman confirmed UCD vice-president for students Martin Butler was hit in the assault.
UCD students' union president Rachel Breslin and Hugh Brady were among those at the protest, where banners were waved to the tune of angry chants.
In a statement, FEE said it would encourage students to take part in demonstrations against cuts in the run-up to the Budget next Wednesday.
"Vulnerable members of society have been targeted consistently throughout this economic crisis," it said.
"Students have been a part of this attack, leading to mass graduate unemployment and emigration. We vehemently oppose this approach by Fine Gael and Labour."