About 200 people showed up to express their support and share their feelings on what the church meant to them.
Former ministers said prayers and parishioners, past and present, who were unable to attend due to age and health reasons, sent messages of support.
Last September, the congregation voted unanimously to dissolve as a group due to dwindling numbers and corresponding cost increases.
Ownership and responsibility for the church that served as its base for 135 years will be transferred to the Southern Presbytery and Synod of Otago and Southland.
Rose Luxford, the moderator of the Southern Presbytery and minister of St Paul's Church, Oamaru, led the final service.
She said the church had served the community for generations.
"Its legacy will live on in the lives and hearts of many.''
Former minister of the Waiareka-Weston Presbyterian Church, and later Columba, the Rev Nancy Parker, said Saturday was a "huge'' day for the congregation.
She said Columba's closure mirrored what was happening to other social groups also facing declining numbers.
"I think it shows us how much the culture has changed. It's not just churches, it's [other examples like] the Lions Clubs, service clubs. We're a more individualistic culture.''
Southern Presbytery executive officer Alan Judge said religions of all faiths across Western society were having to address declining congregation numbers.
He said no decision had been made on the future of the Columba church building.
