Mr Pyne took two questions on the ABC's Q&A program from university students who identified themselves as members of the Socialist Alternative.
One heckled the minister as he tried to answer questions about whether he'd like to see Australia's university system become more like that of the United States.
Then a group behind the guest panel unveiled a banner and chanted: "no cuts, no fees, no corporate universities".
The program producers had to cut away to a clip of a song recorded on a previous episode while order was restored.
"Does this mean you won't have me again?" Mr Pyne asked host Tony Jones.
A recent review of demand driven funding and the national commission of audit have sparked fears among students that the government may deregulate university fees or make other changes which would drive up course prices.