St Botolph's Church, known as Boston Stump, was badly damaged following a tidal surge in 2013 that hit the Lincolnshire town of Boston.
The floodlights were replaced but the switch-on was put in doubt when two lights were stolen.
Reverend Alyson Buxton said it was "fantastic" to see the church lit up.
"We've all been so excited for this moment," she said.
"It's wonderful to see so many people here who've had a wonderful service inside. There's at least 400 people here so it's absolutely fantastic."
The lights were switched on by BBC Radio Lincolnshire presenters Carla George and Scott Dalton.
Peter Sherlock, who gave the church Â£2,000 to reinstall the stolen lights, was among those present and said the service was "very moving".
He is still offering a reward of Â£2,000 for information about who stole the lights.
Matt Warman, the Boston and Skegness MP, was also there.
"A lot of Boston's heritage is about this building and it's hugely significant for everyone," he said.
"It's been a long time since the floods that turned these lights off and I think people are now finally starting to see that we are able to get past that and to show people that Boston is unquenchable."
The exterior of a church known for its tall tower has been lit up for the first time in two years after it was flooded.