Immense dark storms on Neptune were first discovered in the late 1980s by NASA's Voyager 2 spacecraft, according to the Hubble team.
Hubble found two dark storms that appeared in the mid-1990s and then vanished. This latest storm was first seen in 2015, but is now shrinking.
Like Jupiter's Great Red Spot (GRS), the storm swirls in an anti-cyclonic direction and is dredging up material from deep inside the ice giant planet's atmosphere.
The elusive feature gives astronomers a unique opportunity to study Neptune's deep winds, which can't be directly measured.
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"The particles themselves are still highly reflective; they are just slightly darker than the particles in the surrounding atmosphere," said Joshua Tollefson from the University of California at Berkeley in the US.
Unlike Jupiter's GRS, which has been visible for at least 200 years, Neptune's dark vortices only last a few years. This is the first one that actually has been photographed as it is dying.
"We have no evidence of how these vortices are formed or how fast they rotate," said Agustin Sanchez-Lavega from the University of the Basque Country in Spain.
The dark vortex is behaving differently from what planet-watchers predicted.
"It looks like we're capturing the demise of this dark vortex, and it's different from what well-known studies led us to expect," said Michael H Wong of the University of California at Berkeley.
"Their dynamical simulations said that anticyclones under Neptune's wind shear would probably drift towards the equator. We thought that once the vortex got too close to the equator, it would break up and perhaps create a spectacular outburst of cloud activity," said Wong.
That may be related to the surprising direction of its measured drift: toward the south pole, instead of northward towards the equator, researchers said.