Salman's defense attorneys had submitted a motion asking for the judge to grant her a bond, arguing in part that Salman did not know the extent of her husband's plans.
Salman moved to California after the shooting to be closer to her family.
The court order officially revokes U.S. Magistrate Judge Ryu's order for Salman's conditional release granted last month in California.
Salman's husband, Omar Mateen, pledged allegiance to the Islamic State during the attack at the Pulse nightclub last June 12.
Earlier this month, California magistrate Donna Ryu chose to release Salman on $500,000 bail (468,000 euros), ruling that she posed no danger to the public and was not a serious flight risk.
Mateen was killed by police during a shootout at the end of a three-hour standoff.
A hearing has been set for April 10, at which time the government will seek to have her transferred to custody in Florida.
Ryu ruled that Salman, 31, is not unsafe and there is no proof that she has ties to the Islamic State group or holds extremist views, but an Orlando judge ruled that Salman should remain jailed.
The Orlando massacre was the deadliest mass shooting in modern United States history and the most lethal attack on American soil by Islamist militants since the 9/11 attacks. She pointed out that Salman made her admissions to the Federal Bureau of Investigation after a 16-hour interrogation without an attorney.
On June 6, Salman and Mateen were driving around City Place, a retail complex in West Palm Beach, Byron wrote, recounting what Salman told FBI investigators in an 18-hour interview after the attack. A federal judge in Florida on Friday ruled in favor of prosecutors in revoking a bond order that had been granted by judge in California. Her actions on June 11 - she bought Mateen a card for Father's Day and told her family that the couple was planning a trip to California that summer - prove it, she says. As they left, Mateen asked Salman another question.
The conditions of Salman's release in California included house arrest and Global Positioning System monitoring at the home of her aunt and uncle in Rodeo.
Salman's attorney Charles Swift said in a statement that his client maintains her innocence.
Salman pleaded not guilty to the felony charges at a January 18 arraignment. She faces life in prison if she is convicted.
She could not be reached for comment late Friday.