The midday reinstatement came after a chaotic few hours earlier on Thursday when the journalists continued to be blocked from entering the White House grounds.
That prompted the three news organisations to request an immediate hearing before US District Judge Tim Kelly, who issued his decision overnight.
Kelly, acting in a lawsuit brought by CNN, MS NOW and Politico on Monday, ordered a halt to Trump's ban for 14 days in a press freedom case that has played out over the past week in the courtroom and White House grounds.
Kelly said that the revocation of the White House credentials of the reporters "likely violated their constitutional due process rights".
The judge, who Trump appointed in 2017 during his first presidential term, also raised doubts about the US Justice Department's national security arguments for justifying the ban, noting that Trump himself had said the action was due to what the president alleged was false or negative coverage.
Hours after Kelly issued his order, CNN, MS NOW and Politico told the judge they remained barred, and asked for the emergency hearing.
Politico said its reporter's credentials were confiscated.
An MS NOW reporter said she was blocked from the White House.
CNN said some of its staff members were denied entry onto the grounds.
In response, Micah Stopperich, the director of press operations at the White House, said in a court filing that the White House began the process of reinstating press badges for affected reporters at 7.25am, and that the "White House press team dropped badges at the entry gate for members of the press to pick up around 9.55am".
Trump announced the ban last Friday on his social media platform, saying those news organisations "shouldn't be able to constantly write or report FICTION and LIES when they're covering the President of the United States".
Trump framed their reporting as a threat to US national security.
The three outlets sued Trump and other members of his administration, saying the ban violated the US constitution's first amendment protections for free speech and a free press, as well as their due process rights.
A coalition of press freedom groups and dozens of news organisations, including Reuters, later filed a legal brief supporting the three news outlets.
Kelly ordered the Trump administration to immediately return the outlets' press passes and stop enforcing the ban for two weeks.
The judge rejected the administration's stated national security concerns.
"The record lacks factual support for defendants' contention that the revocation of plaintiffs' hard passes will in fact protect national security or that national security will be endangered if the court orders their passes reinstated while this litigation proceeds," Kelly wrote.
In a filing on Tuesday, the Justice Department accused the outlets of threatening national security with their coverage, citing stories about US missile stockpiles, construction of Trump's White House ballroom and turnout at the recent Republican midterm convention.
Theodore Boutrous, a lawyer for the three outlets, welcomed the judge's decision in a statement, saying: "This is a strong ruling vindicating freedom of the press, due process and the rule of law. We greatly appreciate the court's swift action."
Following Trump's ban, other members of the White House press pool of reporters who share resources to follow the US president's movements refused to record or disseminate his events until access was restored for CNN, MS NOW and Politico, acting in solidarity with their fellow reporters.
This occurred as Trump spoke at the United Nations and hosts Chinese President Xi Jinping in Washington DC this week, including events at the White House on Thursday.
There were no TV pool cameras set up for Xi's arrival on the White House's South Lawn Thursday morning, and Fox News, MS NOW and CNN did not air the two leaders' arrival ceremony live.
During Trump's welcome of Xi to the White House, the president made a joke to photographers in the Oval Office about the Chinese having the friendliest press corps.
