Hawaii said in court documents filed Tuesday that the updated ban - set to take effect next week - is a continuation of President Donald Trump's "promise to exclude Muslims from the United States".
The court acted in one of two cases pending involving a case brought by the American Civil Liberties Union, which had sued to stop the ban contained in a March executive order.
The International Refugee Assistance Project pushed the court to hear the case.
The ban's challengers argued that the case against the last version should go forward because numerous same travelers and their families are adversely affected - not just for 90 days, but indefinitely. That dispute concerns both the travel ban and a separate ban on refugees, which does not expire until 24 October.
Hawaii, which brought the 9th Circuit challenge, warned the justices that elements of the earlier ban still could be revived, since Trump has said he wants a "much tougher version".
The Hawaii case also challenged a provision of the order that suspended the admission of refugees into the United States for 120 days.
After Trump replaced his order previously, the court delayed the case which was due this Tuesday.
"Explaining that the freeze on the entry of travelers from the six countries "'expired by its own terms' on September 24" and therefore "no longer presents a live case or controversy", the court agreed with the federal government that the 4th Circuit's ruling for the challengers should be vacated. When that happens, the Court seems likely to declare Hawaii moot as well, which will likely vacate previous orders preventing close relatives of people in the United States from being kept out of the country.
Trump furnished a novel command about immigrants last month, and the management had conveyed the court that meant there was no basis for the justices to pass judgment on the old one. It asked the lower court rulings be erased.
One judge has already scheduled a hearing for Monday on a request to block Trump's new order before it kicks in next week.