Nine people died and 57 were injured in the explosion at Frizzell's fish shop on the Shankill Road in west Belfast on 23 October 1993.
One of the IRA bombers, Thomas Begley, was also killed. His accomplice Sean Kelly was badly injured.
In January 1995 Kelly was sentenced for his part in the Shankill bomb and handed nine life sentences.
He was released under the Good Friday Agreement in 2000.
On Wednesday, hundreds of people - including some of the victims' families - came to West Kirk Presbyterian Church for the service of remembrance as the Shankill Road came to a standstill.
Minister David Clawson said: "I am convinced that the best thing for us to do as men and women of the Shankill today is to gather together in community and on the Shankill. To the relatives seated in the middle of the church, know that today we gather around you, inside this building and outside, we embrace you in your pain."
He told UTV the day was an "opportunity to reflect" on the stories and to "move forward in healing and hope".
Wreaths were laid by local schoolchildren at the bomb site and at the Memorial Park, next to the church.
The events coincided with the timing of the explosion 20 years ago, when the two IRA men walked into the fishmongers carrying a bomb just after 1pm.
The IRA would later claim their target was a meeting of the loyalist UDA's inner council in an office upstairs. But, primed with an 11-second fuse, the device detonated before the bombers could escape.
Wednesday's service followed a walk of remembrance through the Shankill on Tuesday night, passing the site of five bombings which claimed 25 lives during the Troubles.
Charlie Butler helped with the rescue efforts 20 years ago, not realising at first that the bodies of three members of his own family - his niece Evelyn, her partner and daughter - were under the rubbles.
"This time 20 years ago I felt so alone," he said. "And today I didn't, today I had, or should I say, we had people around us that loved us and cared us and showed us the support I think that we still need."
Reacting on Twitter, deputy First Minister Martin McGuinness commented that "the sorrow, grief and loss inflicted on all those who lost loved ones in the IRA's Shankill bomb must be acknowledged with humility and regret".
For more on the story of the Shankill bomb victims, survivors and relatives, you can watch the UTV Live Tonight Special here.