Matthew took his life after a long battle with mental illness.
Warren, author of The Purpose Driven Life, took to the pulpit of Saddleback Church, California, to preach the sermon "How to get through what you're going through".
He was joined by his wife Kay in sharing the message at the two Saturday evening worship services.
An additional 6,500 people tuned in to watch the service live online.
"We intend to spend the rest of our lives comforting others with the comfort we've been given," he said.
Pastor Warren shared that although they did not understand everything, they were able to experience peace in the midst of grief because they knew God was with them and loved them.
They also put their faith in God's greater plan and said that they had hope because there was more to the story of life than the battles they face.
"For 27 years I prayed every day of my life for God to heal my son's mental illness ... it didn't make sense why this prayer wasn't being answered," said Pastor Warren.
"When you go through a difficult time, you automatically start to try and find an answer. But explanations never comfort. You don't need explanations; you need the presence of God."
Kay said she was continuing to choose joy even in grief, reflecting on the title of her 2012 book, "Choose Joy".
"What do you do when hope doesn't turn out the way you think it will? You rebuild your hope," she said.
Pastor Warren went on to challenge the stigma of mental illness, urging anyone with similar struggles to get help.
"Any other part of the body, you can have it hurt and there is no shame in it," Pastor Warren said. "If your brain doesn't work right, why do you have stigma? It's just another organ in your body."
The Warrens have devoted the last decade to removing the stigma of HIV/AIDS and said they now felt called to remove the stigma of mental illness.
"If you struggle with a broken brain, you should be no more ashamed than someone with a broken arm," said Pastor Warren. "It's not a sin to take meds. It's not a sin to get help. You don't need to be ashamed.
The sixteen weeks since his son's death mark Warren's longest absence from the pulpit.
The congregation showed their appreciation by giving the couple a standing ovation.