The three judges at the court found that Johnson's request for Queen Elizabeth II to prorogue Parliament between mid-September until October 14, when there would be a Queen's Speech setting out the government's plans for the coming year, was legal.
While the government played the move off as routine, opposition MPs said the timing of the suspension was aimed to limit their ability to block a possible no-deal Brexit before the UK leaves the EU on October 31.
Miller said she was disappointed with the ruling, according to Efe news.
"We are very disappointed with the judgment today. We feel strongly that parliamentary sovereignty is fundamental to the stability and future of our country and is therefore worth fighting to defend," she told the press outside the court in London.
The decision from the judges came shortly after a similar ruling in Scotland.
Miller has previously challenged the government on its Brexit approach.
Following the referendum in 2016, in which 52 per cent of the UK voters opted to leave the EU, then Prime Minister Theresa May decided to invoke Article 50 of the Lisbon Treaty, which would officially notify Brussels of the country's intention to leave and set a two-year negotiation period to manage the departure.
Miller argued that such a move required parliamentary backing. The case went all the way to the Supreme Court, where judges ruled in favour of Miller, dismissing the government's appeal.
The ruling sent shockwaves through the British press, with pro-Brexit media at the time coming under scrutiny for publishing a front page story with a picture of the High Court judges responsible for the case with the headline "Enemies of the People."
Miller herself said she received an onslaught of abuse following the process.
Johnson's powers have been significantly weakened in recent days as he lost his working majority as well as control of the parliamentary agenda.
Opposition parties banded together to push through a bill that would force the government to seek a Brexit extension if it fails to agree on a deal during the European Council summit in mid-October.
It removes the option of no-deal, which Johnson has held onto as leverage in the negotiations.
The Prime Minister fired 21 Conservative MPs who voted against the government and then lost a vote calling for a snap election on October 15.
The leader of the main opposition Labour Party, Jeremy Corbyn, has said that any snap elections could not be held on Johnson's watch.