There have been angry protests in recent months over the so-called parallel trading.
There is huge demand in China for household items, in particular milk powder, from Hong Kong, which is perceived as being both cheaper and better quality
But Hong Kongers say the trade pushes up costs and causes overcrowding in shopping areas, while also complaining about poor behaviour from mainlanders.
China's Xinhua news agency, citing the ministry of security, said the new rules had immediately come in to force.
It said the decision had been made because of concerns that Hong Kong was under strain from the huge numbers of tourists.
Hong Kong's Chief Executive CY Leung welcomed the move, saying he had raised the issue with Beijing in June.
But he cautioned that the "unruly protests" seen in towns close to the border had actually hampered the discussions and "hurt the feelings between the people of Hong Kong and the mainland", the South China Morning Post reports.
Mr Leung warned that existing visas would remain valid, meaning it could take some time for the effect of the change to be seen.