The worst affected districts included Kozhikode, Kannur, Malappuram, Palakkad and parts of Thiruvanathapuram.
What began as a campaign in the social media on Sunday against the brutality heaped on an eight-year-old in Kathua region led to a shutdown on Monday.
Angry demonstrators, some shouting anti-RSS slogans, blocked traffic and force shops to shut.
Buses and other vehicles were stopped from plying on Monday morning. However, traffic resumed after the police chased away the protesters.
The areas affected by the shutdown are known strongholds of the SDPI, including the suburbs of the capital district.
Government offices and banks in the affected areas opened later in the day.
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