Tom Holladay, teaching pastor at the church in Lake Forest, opened the 9 a.m. worship service by saying the congregation would face the tragedy together as a "church family."
Holladay led a prayer for Warren and his wife, Kay, and their two other children.
Warren, the church's lead pastor, did not attend Sunday, a day after the church announced that Matthew Warren committed suicide at his Mission Viejo home.
According to the Orange County Coroner's Office, Matthew Warren died of a self-inflicted gunshot wound.
Rick Warren, the author of the multimillion-selling book "The Purpose Driven Life," said in an email to church staff that he and his wife had enjoyed a fun Friday evening with their son. But their son then returned home to take his life in "a momentary wave of despair."
The pastor added that over the years, his son had been treated by America's best doctors and received counseling, medication and prayers.
"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?'" Warren recalled.
Despite that, he said, his son lived for another decade, during which he often reached out to help others.
Matthew Warren was well known by parishioners, who say he played a big role in a number of local charities. Churchgoers say they will keep the Warren family in their prayers.
Rick Warren founded Saddleback Church in 1980, according to his biography on the church website, and over the years watched it grow to 20,000 members. He and his wife began by holding Bible studies for people who weren't regular churchgoers.
Matthew Warren was the youngest of their three children.
The church hosted a presidential forum in 2008 with Barack Obama and John McCain. Rick Warren was named the top newsmaker of the year for 2009 by the Religion Newswriters Association. That same year, he delivered the invocation at President Obama's first inauguration.
The Associated Press contributed to this report.