Bates said on Friday that this decision was "arbitrary and capricious".
The judge also said in his opinion that he has agreed to delay his ruling to give the Trump administration 20 days "to determine whether it intends to appeal the Court's decision and, if so, to seek a stay pending appeal".
In September 2017, the Trump administration rescinded the DACA program, calling it a litigation risk.
The decision comes as a related case unfolds in Texas, which sets up the possibility of conflicting rulings.
U.S. District Judge John Bates said his decision to order the Obama-era policy be upheld is predicated on the Department of Homeland Security's so-called failure to defend the merits of nullifying the program.
Under DACA, roughly 700,000 young adults, often referred to as "Dreamers", were protected from deportation and given work permits for two-year periods, after which they must re-apply to the programme.
Two other federal courts in California and NY had previously ordered that DACA remain in place while litigation challenging Mr Trump's decision to end it continued. He said that the so-called Nielson memo (the government's memo on why DACA should end) had nothing new in it, and that it totally ignored most of the points made by its critics.
Judge Bates' order would do that. Nearly a million illegal aliens are eligible to apply. Several government appeals are still pending in United States courts.
"A conclusory assertion that a prior policy is illegal, accompanied by a hodgepodge of illogical or post hoc policy assertions, simply will not do", Bates wrote.
The District of Columbia lawsuit was brought by the NAACP, Microsoft and Princeton University.
In his April ruling Bates wrote that if the DHS fails to issue a memo that would prove that the program was unlawful and unconstitutional, as insisted by the government, "the Rescission Memo will be vacated in its entirety, and the original DACA program will be restored in full".
Congress failed to come to any agreement on a law to replace DACA, leaving the recipients, illegal immigrants brought to the United States as children, in a state of uncertainty for almost the past year.