Released in 1998, the Steps track went straight to number one in the UK and sold more copies than the group's three previous singles combined.
Read more: Steps reflect on 25 years in the pop world
The accompanying wedding-themed music video, complete with the now iconic Tragedy dance, was filmed at All Saints church in Harrow Weald, Greater London.
Recently, the 19th century church launched a JustGiving appeal for help after a passageway collapse revealed poor and structurally unsafe foundations — a problem which left the church facing a £50,000 bill.
But help was at hand in the shape of Scott-Lee, who donated £2,000 to the appeal, writing on the page that she "can’t let this be a Tragedy".
The 47-year-old star added: "I hope this helps your beautiful church. Thank you for the wonderful memories! Merry Christmas, love Lisa from Steps x"
Speaking to The Guardian, Scott-Lee said the 150-year-old church "provided a beautiful backdrop" for the music video.
She added: "People say our Tragedy video is iconic and I felt this donation was the least I could do.
"And with lots of people experiencing difficulties right now, I wanted to give something back and help the church at Christmas time.
"I think the church was a lucky charm for Steps, it’s all come full circle in a wonderful way."
Rev John Baker, vicar at the church, said Scott-Lee's donation and the subsequent publicity had led to donations from all over the world, including the USA and as far afield as Australia.
He said: "Everybody’s saying the same, that their lives have been touched by that music video. They don’t want to see the church disappear. I’m so grateful and thanking God for this surprise."
Steps formed in 1997 and were chart sensations, reaching the top five in the UK Singles Chart with 14 consecutive releases and selling more than 22 million records worldwide.
The group parted ways in 2001, but reformed a decade later and have been a presence in the pop world ever since.
Since their reunion, the group has released four albums and embarked on six different headline tours — as busy as they have ever been.
When their 25th anniversary release Platinum Collection reached the top of the UK Albums Chart this year, they became the first British mixed-gender group to get to number one with four albums in four different decades.
Watch: Steps band members reflect on 25 years of pop