Governor Nikki Haley`s staff said the flag would be removed during a ceremony and relegated to the state`s Confederate Relic Room.
"We will bring it down with dignity, and we will make sure it is stored in its rightful place," Ms Haley said.
Police then surrounded the rebel flag with barricades and rope, a siege of sorts that will end today after the banner is furled for the last time at a 10am local time ceremony.
The flag first flew over the statehouse dome in 1961 to mark the 100th anniversary of the Civil War and was kept there as a symbol of official opposition to the civil rights movement.
Mass protests decades later led to a compromise in 2000 with lawmakers who insisted that the flag symbolised Southern heritage, and it was moved to a corner of the statehouse grounds.
But even from that lower perch, the historic but divisive symbol remained clearly visible in the centre of town.
Shooting suspect Dylann Storm Roof, who has not yet entered a plea to nine counts of murder, reignited a debate over the flag`s history as a symbol of white superiority and racial oppression.
Ms Haley moved first, calling on South Carolina lawmakers to vote the flag down. Other Republican lawmakers who have long cultivated the votes of Confederate flag supporters were quickly announcing that other Civil War symbols no longer deserve places of honour.
Ms Haley said the nine pens she used to sign the bill would go to the families of the victims.
South Carolina`s flag removal bill passed easily in the senate, where state senator Clementa Pinckney, the pastor gunned down at the church, had served, but was stalled by debate in the house of representatives as dozens of amendments were proposed.
House members deliberated well into the night, amid anger, tears and shared memories of Civil War ancestors.
Representative Jenny Horne, a white Republican who said she is a descendent of Confederate president Jefferson Davis, scolded her party members for stalling.
"I cannot believe that we do not have the heart in this body to do something meaningful such as take a symbol of hate off these grounds on Friday," Ms Horne said.
The bill ultimately passed 93-27 in the House - well above the two-thirds supermajority needed to make changes to the state`s "heritage" symbols.
Some lawmakers hugged, cried and high-fived, while others snapped selfies and pumped their fists.
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