The yesterday's proposal now is set to go before the House of Representatives, amid growing public demands for the red, white and blue banner to no longer fly outside the legislature in the state capital Columbia.
"It's the right thing to do," said Democratic state senator Vincent Sheheen as he and his colleagues in the Republican-dominated legislature took up the hot-button issue.
For 15 years, the flag has flown alongside a Confederate memorial on the manicured lawn of the Republican-dominated legislature in the southern state where the Civil War erupted in 1861.
Dylann Roof, 21, a suspected white supremacist charged with the killings, has been seen in online photographs flaunting the Confederate flag, which some embrace as a symbol of Southern heritage but others condemn as a banner of racial hatred.
Governor Nikki Haley, a Republican with Tea Party support, spoke out in favour of taking down the flag in the wake of the Charleston shooting.
But by law, the final decision rests with both houses of the Republican-dominated South Carolina legislature, which could resolve the issue before going on its summer break this week.