Wellingtonians took to Facebook with the usual "did anyone feel that shake?" posts.
The rumbling quake could also be felt in the Press Gallery at Parliament.
One Wellington woman described the quake as "not pleasant, stop it".
Despite the co-incidence, GNS seismologist Dr Anna Kaiser said the Seddon quake was unrelated to the jolt off the South Island.
"When you get a big earthquake, you change the stresses in the crust around the earthquake, and that can trigger aftershocks in the vicinity of that earthquake.
"But obviously that's not a mechanism that could explain the earthquake in the Cook Strait because it was too far away to be caused by that kind of stress change.
"While you do have passing quake waves that can cause some activity, there's nothing that we can say to link this."
Rather, the Cook Strait quake was likely another aftershock of November's Kaikoura Earthquake, and these were likely to continue for some time.
There was also nothing to suggest there was any direct link with the major quake that hit Mexico City.
"It's certainly something that can't be scientifically proven."
A woman on the Wellington Facebook page Vic Deals said the window was shaking at her house.
Another man on the page was less concerned.
"10/10 would shake again," he wrote.
Both of this afternoon's quakes struck in areas well recorded to be seismically active.
There have been thousands of aftershocks in the Marlborough area since last year's 7.8 quake, while there has also been some large earthquakes in the zone south of the South Island.
The southern quake happened near a plate boundary where the Australian plate dives below the Pacific plate - the opposite way to how the two plates subduct in the North Island.
Called the Puysegur Trench, this boundary stretches for more than 800km south from the South Island, to a point in the wild and windy Southern Ocean, around 400km west of the Auckland Islands.
Today's event followed a 6.4 quake in July, that struck 190km southwest of the subantarctic Snares Islands and was also felt by people around the South Island.
In 2009, the 7.8 Fiordland earthquake struck close to the northern end of the trench, releasing 25,000 times more energy than the atomic bomb dropped on Nagasaki in 1945 and twisted the South Island, moving Puysegur Pt on the southwestern tip of the island 30cm closer to Australia.
Its remote location, near Dusky Sound, meant there was relatively little damage.
A magnitude 7.2 quake hit the trench itself in November 2004.
"This earthquake was certainly associated with the subduction processes in some way, but the exact fault that it would have been located on is quite hard for us to tell right now.
"The Pacific Rim is obviously a really active margin for earthquakes and volcanoes, and this [subduction zone] is certainly part of that system."
There was much more scientists could learn about the southern quake zone, but its far-flung location had made it a difficult area to investigate.
The Hikurangi Subduction Zone, off the North Island's East Coast and now the focus of a major international project, ultimately posed the greater threat to people.
