Haley, who initiated the bold move, in the aftermath of the tragic shooting of several black people inside a church last month by a white supremacist, was hailed nationally for this effort.
The flag will be removed this morning 10 am local time, and will then be taken to the 'relic room' of a military museum in Columbia.
South Carolina's House of Representatives had passed the vote with 94-20, more than the two-thirds vote needed for approval, paving the way for the removal of the flag.
"When the emotions start to fade, the history of actions that took place by everyone in South Carolina is one we can all be proud of," she added.
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White House Press Secretary Josh Earnest, described it as a good move.
US President Barack Obama had last month praised Haley for her bold move.
"This is a historic day in South Carolina," Senator Lindsey Graham said.
"After the horrific tragedy in Charleston, our state could have gone down one of two paths - division or reconciliation. I am thankful we chose the path of reconciliation," he said.