Warren and his wife Kay revealed their son's death in a letter to the congregation of Saddleback Church in Lake Forest, the Los Angeles Times reported. The Warrens said their son had dealt with depression for much of his life.
Matthew Warren was an "incredibly kind, gentle and compassionate man," they said in the statement. "He had a brilliant intellect and a gift for sensing who was most in pain or most uncomfortable in a room. He'd then make a beeline to that person to engage and encourage them."
The statement said the younger Warren killed himself after spending an evening with his parents, but did not provide details of his death.
"Kay and I've been privileged to hold your hands as you faced a crisis or loss," the statement said. "Today we need your prayers for us."
Rick Warren, the author of "The Purpose Driven Life," who delivered the invocation at President Obama's first inauguration, said only those closest to his son knew he had "struggled from birth with mental illness, dark holes of depression, even suicidal thoughts."
"Today after a fun evening together with Kay and me, in a momentary wave of despair at his home, he took his own life," Warren said.
"Kay and I often marveled at his courage to keep moving in spite of his relentless pain. I'll never forget how, many years ago, after another approach had failed to give relief, Matthew said, 'Dad, I know I'm going to heaven. Why can't I just die and end this pain?' but he kept going for another decade."
The Warrens have two other children, Amy and Josh.
2014: The Year in Music [PHOTOS]