Police and paramilitary forces imposed tight security after Muslim separatists staged a spate of deadly attacks on candidates, party workers and rallies before the elections.
Muslim separatist politicians called for a boycott of the vote. A separatist-sponsored strike took traffic off the streets and all businesses remained shut for the day, residents said.
Civic elections have not been held in Indian-administered Kashmir for the past 27 years, partly because of an insurgency against Indian rule, but also due to fears by the previous ruling National Conference party of creating a rival power base.
The elections started on 29 January in the two northern districts of Kupwara and Baramulla with 49% voter turnout. On Tuesday residents of the summer capital of Srinagar and the winter capital of Jammu voted to elect mayors.
In Srinagar officials said before polling booths closed that more than 20% of voters had cast their ballots.
"The turnout proves people want peace and development," the state's urban development minister Ghulam Hasan Mir said.
In Jammu the turnout was 40% to 45%, officials said. The mainly Hindu city has seen much less violence than other areas during the revolt which began in 1989 and has claimed tens of thousands of lives.
"The turnout proves people want peace and development"
Ghulam Hasan Mir,
Kashmir Urban Development Minister
No major violence was reported on Tuesday, but in the Miasuma district of Srinagar, dozens of youths pelted riot police with stones and burnt car tyres.
On Monday night, an election officer and a policeman were injured in a grenade attack on a polling station in Srinagar's Batamaloo area, police said.
There are about a dozen separatist groups in Indian-administered Kashmir. Most want it to join Pakistan, which rules the other portion of the divided state, while a few seek independence.