The bridge became a landmark in the fight for racial justice when Mr Lewis and other civil rights marchers were beaten there 55 years ago on Bloody Sunday, a key event that helped galvanise support for the passage of the Voting Rights Act.
Mr Lewis returned to Selma each March in commemoration.
Sunday found him crossing alone — instead of arm-in-arm with civil rights and political leaders — after his coffin was loaded on a horse-drawn wagon that retraced the route through Selma from Brown Chapel African Methodist Episcopal Church, where the 1965 march began.
As the wagon approached the bridge, members of the crowd shouted “Thank you, John Lewis!” and “Good trouble!” – the phrase Mr Lewis used to describe his tangles with white authorities during the civil rights movement.
Some crowd members sang the gospel song Woke Up This Morning With My Mind Stayed on Jesus. Later, some onlookers sang the civil rights anthem We Shall Overcome and other gospel tunes.
Mr Lewis died on July 17 at 80, months after he was diagnosed with advanced pancreatic cancer.
Mr Lewis served in the US House of Representatives for Georgia’s 5th congressional district from 1987 until his death.
The wagon rolled over a carpet of rose petals, pausing on the bridge over the Alabama River in the summer heat so family members could walk behind it.
On the south side of the bridge, where Mr Lewis was beaten by Alabama state troopers in 1965, family members placed red roses that the carriage rolled over, marking the spot where Mr Lewis spilled his blood and suffered a head injury.
As a military honour guard lifted Mr Lewis’s coffin from the horse-drawn wagon into a hearse, Alabama state troopers, including some African American ones, saluted Mr Lewis.
Franz and Ellen Hill drove more that four hours from Monroe, Louisiana, to watch the procession.
Franz Hill, 60, said he remembers, as an African American child, watching news footage of Mr Lewis and other civil rights marchers being beaten by law enforcement officers.
“I had to come back and see John Lewis cross the bridge for the last time,” said Mr Hill.
Mr Lewis’s body was then taken to the Alabama Capitol in the afternoon to lie in repose, retracing the route marchers took in the days after Bloody Sunday to demand justice from Alabama Governor George Wallace.
Bertha Surles and Edna Goldsmith stood along the highway between Selma and Montgomery to pay their final respects. Both carried signs, reading “Thank you.”
“He fought for rights up unto his death,” said Ms Surles, 70.
A series of events began on Saturday in Mr Lewis’s hometown of Troy, Alabama, to pay tribute the late congressman and his legacy. He will lie in state at the US capital next week before his private funeral on Thursday at Atlanta’s historic Ebenezer Baptist Church, which the Reverend Martin Luther King Jr once led.
A native of Pike County, Alabama, Mr Lewis became involved in the civil rights movement as a young man.
In 1965, he and other marchers were beaten in Selma. The news coverage of the event helped to galvanise support for the passage of the Voting Rights Act of 1965.
Lewis, 80, died on July 17 several months after he was diagnosed with advanced pancreatic cancer.