Manuel Valls came under pressure after using a government Falcon jet to take two sons to the match on Saturday.
He insists he was on an official trip to discuss the Euro 2016 championship, which France is hosting.
But Mr Valls said he was sensitive to public reaction and agreed to pay the costs for his children.
Speaking on a visit to the French island of Reunion in the Indian Ocean, the PM said the trip was "nothing out of the ordinary" and stressed that his sons' presence added nothing to the cost.
But he said France had "no need for a pointless controversy" and "to remove any ambiguity, I decided to assume the cost of the trip for my two children".
The whole cost of the journey is said to have been around €20,000.
Aides close to Mr Valls said the €2,500 payment was based on the average price of taking a commercial flight for the round trip from Poitiers to Berlin.
However some commentators said the cost of hiring the Falcon jet, along with the security provision required, would be much more.
The prime minister says he travelled to the Champions League final to meet Uefa President Michel Platini to discuss issues such as Euro 2016 and the Fifa corruption scandal.
But the use of a government plane to transport him and his sons to see Barcelona beat Juventus 3-1 prompted disbelief.
Born in Barcelona, Mr Valls is a supporter of the European champions.
Earlier this week opposition MPs called on Mr Valls to pay back the cost of the flight, and he faced a series of jibes in the National Assembly.
The scandal sparked a storm of reaction on social media, with the hashtag #Vallsgate trending in France on Wednesday.
Correspondents say the row has threatened to overshadow major reforms aimed at softening labour laws for small and medium-sized businesses and adding tens of thousands of jobs to the labour market.
Under the "Small Business Act", businesses with no employees would be granted €4,000 (£2,920; $4,500) for giving their first worker a year-long contract.
Unemployment in France is at 10% and Mr Valls also proposed that employers should be allowed to extend temporary contracts up to a maximum of 18 months.
France's prime minister says he will pay €2,500 (£1,825) for taking his children on a controversial trip to the Champions League final in Berlin.