The US says it has "an increasing list of problems" with Syria, hours after Damascus formed a "front" with Iran.
Ms Scobey's recall is a "strong signal" of US displeasure with Syria
Secretary of State Condoleezza Rice told a Senate hearing that she had withdrawn the US ambassador to Syria to send a strong signal of displeasure.
Ambassador Margaret Scobey was first pulled out of Damascus for talks, but there is now no date for her return.
Washington insists Syria's problems are not just with the US, but with the whole international community.
Tension has increased since former Lebanese Prime Minister Rafik Hariri, who had called for the withdrawal of Syrian troops from the country, was killed in a bomb attack in Beirut on Monday.
Syria and Iran, which is also under pressure from the US, said on Wednesday that they would co-operate more closely to meet challenges and threats.
Ms Rice told senators that ambassador Scobey had been withdrawn from Damascus for an "indeterminate" time as a sign of strong US displeasure with Syria following the apparent assassination of Mr Hariri.
"The proximate cause was Lebanon, but unfortunately we have an increasing list of problems with Syria," she told the Senate Foreign Relations Committee.
Rafik Hariri had called for Syria to remove its troops from Lebanon
She said the recall of Ms Scobey on Tuesday sent a "very strong signal", but refused to say how long the ambassador would stay away.
"But we will make known there are steps that we would like to see taken," she added.
She said that, while it was not known who carried out Monday's attack, Syria - with its influence in Lebanon - had a "special responsibility for the kind of destabilisation that happened there".
Many of the hundreds of thousands who attended Mr Hariri's funeral in Beirut on Wednesday blamed the Syrians for his death.
Iran has said it is ready to help Syria "on all grounds to confront threats".
Tehran has been accused by the US of seeking nuclear weapons.
"Our Syrian brothers are facing specific threats and we hope they can benefit from our experience," said Iranian Vice-President Mohammad Reza Aref.
White House spokesman Scott McClellan responded: "Their problem is not with the United States, it's with the international community. Both Syria and Iran... need to abide by the commitments they have made."
Syria has denied any involvement in the massive bomb attack that killed Mr Hariri, and has stressed that its common front with Iran is not an alliance against Washington.
"We are not the enemies of the United States, and we do not want to be drawn into such an enmity," Syria's ambassador in the US, Imad Moustapha, told CNN.
BBC diplomatic correspondent Jonathan Marcus says the Syrian authorities are looking increasingly isolated, with only the Iranians speaking up on their behalf.
Washington lists Syria as a sponsor of terrorism and has accused Damascus of contributing to instability in Lebanon.
Sanctions have also been considered because of Syria's refusal to comply with a United Nations resolution to withdraw its 14,000 troops from Lebanon.