George and Barbara met when she was just 16, and he 17.
More than 1,500 friends and family members attended the private service at the church, which was the Bushes' place of worship for many years.
Family and friends gathered Saturday to remember Barbara Bush, celebrating the life and legacy of the former first lady.
Former Florida governor and presidential candidate Jeb Bush joked about his mother's famously no-nonsense demeanor. Theirs was the longest marriage of any presidential couple. Bush's only living daughter, Dorothy Bush Koch, could be seen with her arm around her father.
The funeral program shows that her grandchildren will also play prominent roles: her granddaughters will offer readings during the service and her grandsons will serve pallbearers.
The Bush family was seated in front of the church.
Other presidents also have not attended the funerals of former first ladies.
It was also historic for the city of Houston.
Barbara Bush, wife of the nation's 41st president and mother of the nation's 43rd, died Tuesday at her Houston home, aged 92.
George H W Bush followed in his wheelchair, pushed by son George W Bush, shaking hands with those in the pews.
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The burial was on the grounds of the Bush library at Texas A&M University in College Station, about 100 miles northwest of Houston. Hundreds of people lined both sides of the street near the campus ahead of the service.
Among the other roughly 1,500 guests were former Rep. Invited guests included former secretary of state Condoleezza Rice, actor Chuck Norris, broadcaster Brit Hume, and Karl Rove, George W. Bush's former senior adviser and White House deputy chief of staff.
Mr Trump had said he was staying away to "avoid disruptions due to added security" but added that he would be watching the funeral.
In another nod to the former first lady, many women wore pearl necklaces to the funeral, a clear acknowledgment of her signature accessory.
On Friday, more than 6,200 people visited the Houston church during a public viewing. "Our mom was our first and most important teacher", he said.
Thousands of mourners paid respects to Barbara Bush ahead of the memorial on Friday, as casket lay in repose inside the church.
Guests have begun to arrive at St. Martin's Church in Houston for the funeral of former first lady Barbara Bush. Former President George H.W. Bush made a last minute decision to greet mourners at the church. He was among four former US presidents at the service. She was 3 when she died of leukemia in 1953.
From there, it turned toward the back of the library, where the procession came to an end.
George H.W. Bush, whose health is shaky, was wheeled into the service by George W. Bush.