The Maoist-led 30 party alliance had initially vowed to enforce shutdown till Thursday but decided not to extend the three-day strike after widespread public criticism over the disruptions and trouble.
Nearly half a dozen vehicles were vandalised and dozens of people were injured during clashes with the police here.
The police resorted to baton charge and fired tear gas cells to disperse the agitators at Bijulibazaar.
Four security personnel were also injured in the clashes.
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The meeting of 30 opposition parties including the UCPN-Maoist, Madhesi Front and fringe ethnic parties, held this evening to review the protest programme, decided not to extend the strike for two more days realising that the people would not back their protest.
"After considering suggestions from the public and business community, we have decided to call off the strikes tomorrow and the day after," said opposition alliance spokesperson Prem Bahadur Singh.
They are opposed to government's move to promulgate the constitution through voting process, demanding consensus on the key issues such as federalism and forms of governance.
People also expressed their anger and resentment on the social media against the Maoist-led shutdown.
"Why not stage hunger strike by the leaders themselves instead of causing hardship to the people to press for their demand," wrote one commentator on the facebook page of a Maoist leader.
Earlier in the day, the agitators also burnt a taxi in Koteshwor area of Kathmandu.
A passenger bus was also set ablaze in Jaleshwor Municipality in southern Nepal.