Local media reported two deaths in those clashes.
The atmosphere seemed to have cooled down on Wednesday morning, but heavy security was in place across the capital, especially outside the so-called police line where the special court would be convened.
Authorities also ordered the closure of schools across the country, and continued to restrict access to social media platforms such as Twitter and Facebook.
“At a time when we are already struggling to feed our children, further uncertainty has arisen,” van driver Farooq Bhatti told AFP in Rawalpindi on Wednesday morning.
“Violence will do no one any good…everyone will be affected…but I doubt the decision-makers care.”
PTI vice-chairman Shah Mahmood Qureshi urged supporters to continue protesting in a “legal and peaceful manner”, adding that the party’s lawyers would file several appeals and petitions against Khan’s arrest.