The storm, the most disruptive to hit Earth since 1989, was unleashed by the fourth-most powerful solar flare yet to be seen, NASA said.
However, it caused no large power outages or other major problems.
The gigantic cloud of highly charged particles hurled from the sun, posed a threat to electric utilities, high frequency radio communications, satellite navigation systems and television broadcasts.
Continued turbulence on the sun remains a concern for the next week, space forecasters say.
The biggest immediate effect was the blackout of high-frequency voice-radio communications for planes, flying far northern routes.
But airliners in an emergency could still communicate through VHF contact with another aircraft or military monitoring station.
British controllers were keeping trans-Atlantic jets on more southerly routes than usual to avoid the problem.
The particle storm, measuring 13 times larger than Earth, was rated a G5, the highest intensity on scientists' scale of space weather.
Space observers have measured G5 storms five times in the past 15 years, but few of them have hit Earth so directly.
"It is extremely rare to get this level of geomagnetic storming... This is one of the strongest storms that we have received during this cycle"
The National Oceanic and Atmospheric Administration
Magnetic field collision
The storm whipped through the solar system at about 8 million kph, taking just 19 hours to travel the 150 million km from the sun to envelop the planet.
Federal scientists said it collided with Earth's magnetic field at 0613 GMT on Wednesday, about 12 hours earlier than predicted.
Such storms pose no direct threat to people on the ground, because the Earth's thick atmosphere deflects and absorbs incoming charged particles.
But the storm may produce colourful auroras in the northern night sky visible as far south as El Paso, Texas, beginning late on Wednesday.
The last time a G5 storm hit Earth was in 1989, which damaged the power grid and caused electrical blackouts in the Canadian province of Quebec.
"It is extremely rare to get this level of geomagnetic storming," said Larry Combs, forecaster for the Space Weather Center at the National Oceanic and Atmospheric Administration in Colorado.
"This is one of the strongest storms that we have received during this cycle."
There were few immediate reports of damage related to the geomagnetic storm. However, Combs said, "We know that our power grids are definitely feeling the effects of this."
That is because disruptions in the magnetic field caused by the incoming particles can induce power surges and other current fluctuations in electrical systems.
Geomagnetic storms have caused power disturbances in the United States and Canada, at least 11 times since 1940.
International space station
The increased solar activity is also affecting the International Space Station.
The Expedition 8 crew, Commander Mike Foale and Russian cosmonaut Alexander Kaleri, briefly retreated to the aft end of the station's service module, which is shielded from higher levels of radiation.
The pair will spend about 20 minutes there, twice on each orbit of the Earth for about three orbits, until the station phases out of the high radiation areas.
Increased radiation levels
affected crew at the ISS
In Tokyo, Japanese space agency officials, already forced to temporarily shut down one satellite, said on Thursday they had lost contact with a second satellite that might have been effected by the solar flare.
"We have completely lost touch with the Midori 2, and don't know what's going on with it," said Junichi Moriuma, a spokesman for the agency, known as JAXA. He said the agency was trying to restore communications.
"At this point, we don't know if there is a relation between this accident and the solar flare," he said. "We are still in the process of figuring out what caused the problems."
Space scientists in the United States and Europe, as well as commercial satellite operators, shut down some delicate instruments and turned them away from the storm's blast. Solar panels are particularly vulnerable.
Researchers said Earth was protected from the storm's full impact because the magnetic field of the storm cloud was pointed north in the same direction as Earth's magnetic field.
But if the cloud's magnetic field shifted southward - something that still could happen - its opposing force would, in effect, open a "hole" in the planet's magnetic shield.
That could result in later disruptions to electrical systems, they said.