The dawn-to-dusk strike call was given by the Kerala Vyapari Vyavasyi Ekopanasamiti and Vyapari Vyavasayi Samiti, leading retailers' outfits in the state.
Reports from across the state said the response to the protest call was total with small, medium and wholesale outlets remaining closed.
Leaders of the trade bodies said the move would "grievously harm" about 1 million shop owners and another 2.5 million shop and business establishment workers in Kerala.
They wanted the Centre to roll back the decision and the state government to use its powers to ensure that the retail sector was not opened up to big international players.
The Centre's decision to allow 51 per cent FDI in multi party retail and 100 per cent FDI in single brand retail is being opposed by opposition parties and various state governments, who have said the move would harm millions of small traders and cause huge unemployment in the rural areas.