CHARLESTON, South Carolina — Singing the words to “Amazing Grace” in a deep and powerful baritone, President Obama delivered an impassioned eulogy to honor the life of Rev. Clementa Pinckney and the tragedy of his fatal shooting — a historic moment from the nation’s first black president in addressing the “uncomfortable truths” about prejudice and racial bias still alive in America.
The president spoke before thousands of mourners gathered across Charleston on Friday to pay their final respects to Pinckney, one of the nine people fatally shot in the massacre at Emanuel African Methodist Episcopal Church during a prayer session last week.
“Maybe we now realize the way racial bias can affect us even when we don’t realize it,” Obama said, drawing the crowd to their feet. “So that we search our hearts when we consider laws that make it hard for some of citizens to vote. By recognizing our common humanity, by treating every child as important regardless of the color of their skin and the station into which they were born and to do what is necessary to make opportunity real for every American.”
Obama honored Pinckney’s influence as a beloved church leader and state senator who offered his life to public service since he was first elected to the South Carolina legislature at the age of 23.
“We are here today to remember a man of god who lived by faith. A man who believed in things not seen. A man who believed there were better days ahead off in the distance,” Obama said. “What a life Clementa Pinckney lived, an example that he set. A model for his faith.”
RELATED: Charleston mayor: This is a historic moment
Mourners started gathering for the service here long before dawn, with crowds soon swelling to the thousands outside the TD Arena in downtown Charleston. It didn’t take long for the 5,200-person arena to reach full capacity, leaving thousands to tune in at spillover spaces throughout the city.
Friends, former colleagues and religious leaders spoke for the hours-long service, sharing stories of Pinckney’s big heart and gentle voice. First lady Michelle Obama and Vice President Joe Biden were in attendance, as well as former secretary of state and Democratic presidential candidate Hillary Clinton. A bipartisan group of lawmakers joined the president on Air Force One to attend the service, including House Speaker John Boehner and Reps. Elijah Cummings and John Lewis.
A program for the service was lined with photos of Pinckney and his loved ones, including heartfelt messages from his family. “I know you were shot at the Church and you went to Heaven. I love you so much!” Pinchney’s daughter Malana wrote, signing the note, “Love your baby girl and grasshopper.”
Earlier in the day, supporters and congregants from across state lines convened at the historic black church, commonly referred to as Mother Emanuel, to watch the procession as a hearse carried Pinckney’s body away. Pinckney, a 41-year-old father of two, was named pastor of the church in 2010.
All nine victims were shot to death last Wednesday after the admitted gunman, 21-year-old Dylann Roof, entered Mother Emanuel and attended a weekly prayer session. Witnesses said that Roof singled out Pinckney and asked to sit next to the pastor. Police said Roof then remained at the session for an hour before opening fire.
According to witnesses, Roof told the congregants, “you are raping our women and taking over our country” before he gunned them down.
Federal authorities are now investigating the shooting as a hate crime. Meanwhile, photos have surfaced of Roof posing with Confederate flags and along with a manifesto allegedly attributed to him preaching white supremacy.
The symbol of the Confederate battle emblem has been central to discourse in the aftermath of the massacre. At the urging of South Carolina Gov. Nikki Haley, the state legislature has moved to remove the Confederate flag — representing the racially-charged darkness of America’s past — and no longer see it fly over the statehouse grounds.
Obama spoke candidly about the symbolism behind the Confederate battle emblem and how last week’s events have exposed the pain that its flag represents for so many U.S. citizens.
“As we all have to acknowledge, the flag has always represented more than ancestral pride,” Obama said. “For many, black and white, the flag was a reminder of systemic oppression and racial subjugation.”
“We see that now,” he added.
Speaking at the Pinckney’s funeral, state Sen. Gerald Malloy attributed the historic move to his former colleague.
“Clem all the change you wanted to see, all the change you wanted to do, and all the things we talked to, because of you, we will see the Confederate flag come down here in the state of South Carolina,” Malloy said.
Obama spoke to the history and significance of the black church, how its doors were hush harbors for slaves, praise houses for their descendants, bunkers for civil rights fighters and community centers for generations today.
“To the families of the fallen, the nation shares in your grief. Our pain cuts that much deeper because it happened in a church,” Obama said. “The church is and always has been the center of African-American life. A place to call our own in a too often hostile world. A sanctuary from so many hardships.”
A day earlier, the funerals for two other victims in last week’s massacre were held in Charleston. Ethal Lance, a 70-year-old church custodian, and Sharonda Coleman-Singleton, a minister and high school track coach, were laid to rest.
RELATED: Unity and grace in Charleston after attack
In a rare move for a president who often declines to discuss ongoing investigations, Obama on Friday condemned the hatred and meaning behind Roof’s violent act.
“Blinded by hatred the alleged killer could not see the grace surrounding Rev. Pinkney and that bible study group. The light of love that shone as they opened the church doors and invited a stranger to join in their prayer circles,” Obama said.
Trymaine Lee
Trymaine Lee is an NBC News correspondent.
Amanda Sakuma