The apparently unremarkable painting was found hanging in Holy Trinity in Bradford-on-Avon, Wiltshire, in 2006 and identified as Quentin Metsys' Christ Blessing.
Given to the church in 1940 by a couple from the nearby village of Holt, the small oil was sold for about £1.5m.
The church has now reopened after the year-long revamp.
The small oil panel depicting Jesus was discovered in the Norman church by art conservator Kiffy Stainer-Hutchins and art historian Simon Watney a decade ago.
Painstaking research found it to be the work of Metsys - an influential painter who worked in Antwerp in Belgium in the 16th Century.
Further investigation also found the work was one half of a larger work that had been sawn in two - the other part depicted the Virgin Mary at prayer.
Churchwarden Judith Holland said 75% of the windfall had contributed towards the much-needed restoration work at the church.
"It was such a gift and such a blessing," she said.
"We've put in under floor heating, new lighting and moved the font so it's very spacious and the whole building has been cleaned - and the difference is amazing.
"Some people - if they've been worshipping there for many years - suddenly it's all changed and that can take a while to get used to but on the whole it's been a positive feedback."
The church re-opened on Tuesday for its annual Christmas Tree Festival of 60 decorated trees representing the schools, businesses and groups from across Bradford-on-Avon.
A church has undergone a £2m refit thanks to the discovery of a long-lost Flemish masterpiece in a side-aisle.