Flanked by law enforcement officials and by the parents of children who were killed by people in the country without documentation, Trump on Friday maintained that he was not through fighting for his signature campaign promise, which stands largely unfulfilled 18 months before voters decide whether to grant him another term.
"Congress has the freedom to pass this resolution," Trump said, "and I have the duty to veto it."
A dozen defecting Republicans joined Senate Democrats in approving the joint resolution on Thursday, which capped a week of confrontation with the White House as both parties in Congress strained to exert their power in new ways.
On Thursday, Trump tweeted "VETO!", following the Senate vote.
It is unlikely that Congress will have the two-thirds majority required to override Trump's veto, though House Democrats have suggested they would try nonetheless.
After Trump signed the expected veto, US House Speaker Nancy Pelosi said the body planned to vote for a veto on March 26 and potentially override Trump's move.
The president wants to use the emergency order to divert billions of federal dollars earmarked for defence spending towards the wall along the southern border with Mexico.
His plan still faces several legal challenges from Democratic state attorneys general and environmental groups that argue the emergency declaration was unconstitutional.
Those cases could block Trump from diverting extra money to barrier construction for months or longer.
The American Civil Liberties Union (ACLU), which filed one of the cases, said the veto was meaningless - like the declaration in the first place.
"Congress has rejected the president's declaration, and now the courts will be the ultimate arbiter of its legality," said ACLU Executive Director Anthony Romero. "We look forward to seeing him in court and to the shellacking that he will receive at the hands of an independent judiciary."
Trump said the situation on the southern border was "a tremendous national emergency", adding that "our immigration system is stretched beyond the breaking point".
Trump is expected to issue his second veto in the coming weeks over a congressional resolution seeking to end US backing for the Saudi-led coalition fighting in Yemen.
The resolution was approved in the aftermath of the killing of US-based Saudi journalist Jamal Khashoggi in the Saudi consulate in Istanbul on October 2, 2018.