The quake's epicentre was at the top of the South Island at a depth of 22 kilometres, the USGS said. New Zealand's official GeoNet monitoring service put its intensity at magnitude 5.2.
Wellington is separated from the quake's epicentre by the Cook Strait and the temblor was felt in the capital as two distinct jolts, a few seconds apart, that shook windows.
The fault that generated the seismic tremor is the same one that caused two 6.5-magnitude quakes in July and August 2013, which caused power cuts and sent panicking Wellington office workers fleeing into the streets.
The capital was the scene of the country's most powerful earthquake in 1855, an 8.2-magnitude monster that caused four deaths and changed the city's entire geography, pushing the shoreline out 200 metres (660 feet) as it thrust the harbour floor upwards.
New Zealand is on the boundary of the Australian and Pacific tectonic plates, forming part of the so-called "Ring of Fire", and experiences up to 15,000 tremors a year.