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."

Aaron Saucedo, 23, had already been charged with murder in connection with a killing in August 2015, police say.
Now he has been linked to the deaths of eight other people, between January and July 2016.
Police say they have not identified a motive but believe he acted alone. His lawyer has not commented.
The 2015 victim was a 61-year-old man who had dated the suspect's mother, Phoenix Police Chief Jeri Williams said.
The other victims, including a 12-year-old girl and a 55-year-old woman, seem to have been targeted at random.
"Today is a good day in the city of Phoenix," Mayor Greg Stanton said.
Police gave few details on how they linked the man to the killings, which stopped last July amid extensive media coverage.
But they said the evidence included surveillance video, witness statements and ballistics material.
He faces 26 additional felony counts, including multiple counts of homicide, aggravated assault and drive-by shootings.
The Maricopa County attorney has not yet decided which charges to formally bring against him.

The 31-year-old had publicly revealed she was expecting her third child during a concert in May.
A statement on her Twitter account on Monday said: "Charlotte and Jonny are very sad to announce that they lost their baby. Now is a time for grieving and being together as a family.
"We kindly ask everyone to respect that peace."
The Cardiff-born star and her partner, musician Jonny Powell, have been together for seven years.
She is already a mother to nine-year-old Ruby and Dexter, eight, from her previous relationship with Gavin Henson.
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.
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Police in the US state of Arizona say a man arrested last month is responsible for a series of deadly shootings in Phoenix last year.
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Singer Charlotte Church has lost her unborn baby, she has announced.