Calls from the anti-government activists for city-wide action led to the targeting of road and rail services, reports the South China Morning Post newspaper.
Earlier, protesters had promised the "dawn of anti-epidemic" action if the government did not close the border as part of its response to the coronavirus, which has so far killed 132 people in China.
The disruption came a day after Chief Executive Carrie Lam revealed that her government would reduce cross-border travel with the rest of China through measures such as the suspension of new visas to individual mainland tourists and the shutdown of two railways, including the Hong Kong section of the Guangzhou-Shenzhen-Hong Kong Express Rail Link.
Apart from the rail service suspensions, announced by the government on Tuesday and effective from midnight on Thursday, flights to and from China would also be cut by half and cross-border bus services reduced.
But Lam stopped short of the total closure of the city's borders demanded by legislators from across the political spectrum.
Wednesday's low-level strike action came with Hong Kong in the grip of anti-government unrest, sparked last June by the now-withdrawn extradition bill.
The protests, which often descend into violence, have since morphed into a wider set of anti-government grievances, fuelled by allegations of police brutality and the campaign for more democracy.
( With inputs from IANS )