Bruce Buckingham, a spokesman for the agency, told reporters in Cape Canaveral on Tuesday that "we are going back to the pad".
Buckingham said Ernesto "is going to be less intense than first thought and it does not exceed our [wind] requirements to be at the pad".
The shuttle's return to the launch pad rekindled hopes that Atlantis can be successfully launched before the current window to do so closes on September 7.
The window is determined by various technical factors including the position of the space station, the angle of the sun and newly imposed restrictions by Nasa to launch only during daylight so cameras can have clear views of the shuttle's external fuel tank.
It would be the first International Space Station assembly mission undertaken by Nasa since the Columbia accident in 2003.
The shuttle had begun what was to be a laborious day-long journey back towards its hangar on Tuesday morning in order to protect it from rains and high winds generated by Ernesto.
However, while Ernesto is still forecast to pass near Cape Canaveral later in the week, it is no longer expected to be strong enough to threaten the $2 billion shuttle, or a $372 million station power module packed in its cargo bay.
The September 7 deadline also is due to a planned Russian launch of a Soyuz re-supply ship to the space station.
Nasa had asked about delaying the capsule's flight to buy more time for a shuttle launch but programme managers said on Tuesday that option was unlikely due to technical reasons.
The next launch opportunity for Atlantis would have been in late October.