Hundreds of people have protested over the increase in public transport costs.
The Pakistani government has already rescinded the fare hike, backing down soon after the protests began on Thursday.
Police said that many of those taking part in Friday's protests were students, demanding the release of demonstrators arrested in the previous protests.
"Yesterday people came out to protest against an increase in transport fares, but today [Friday] they came out with a vengeance, pelting stones at police ... the police had to call in reinforcements," Kamal Hyder, Al Jazeera's correspondent in Islamabad, said.
"Because the rioting is taking place, just on the outskirts of the city straddling a main intersection that connects other cities to Islamabad and to the airport it is causing huge problems for commuters."