The initial estimate, before August, was 2 to 3 per cent.
The year-on-year figure for the third quarter showed a drop of 2.9 per cent, the biggest year-on-year contraction in a decade.
Earlier this month, Financial Secretary Paul Chan Mo-po warned a further downgrade for 2019 might be "unavoidable" and there was a "very big chance" the city would be in recession for the whole year.
Hong Kong has increasingly has become a battleground between police and protesters since June, when mass peaceful marches targeted a government proposal, since shelved, to allow the city's criminal suspects to be extradited to mainland China.
Those protests have since morphed into a larger activism, with citizens demanding the right to vote for their own city leaders.
This week, the pro-democracy protests have taken a dark turn. On Wednesday, a 15-year-old boy was hit in the head by what appeared to be a tear-gas canister, according to the city Hospital Authority.
A day earlier, a battle between police and protesters turned a top university's campus into a combat zone.
On Monday, a Hong Kong police officer shot a protester, while in a separate incident, protesters apparently set on fire a man who had expressed support for police outside an MTR station.