The Prince of Wales and the Duchess of Cornwall were among those at the event at St Paul's Cathedral in London.
Representatives of the UK's armed forces and all countries involved in the battle were in attendance, as well as descendants of men who fought in it.
The battle at Waterloo cost thousands of British and allied lives in the defeat of Napoleon's forces.
Nearly 180,000 men fought for more than 10 hours, with more than 35,000 horses and some 500 cannon on the two sides.
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The service, which was also attended by Prime Minister David Cameron, is part of a series of events marking the anniversary.
The Earl of Wessex, the Duke and Duchess of Gloucester, and the 9th Duke of Wellington were also among the congregation.
Some 200 children and 200 teachers were invited, along with members of the public who entered a ballot for tickets.
British soldiers in full military regalia stood to attention outside the cathedral as guests went in.
Squadron Sgt Maj Tony Gray, 76, of the Light Cavalry, said: "This anniversary means a great deal.
"The battle changed history. Had we not won, we probably would be speaking French now."
Extracts from accounts of the battle were read at the service by British, French and German readers.
A commemoration service, attended by the Duke of Kent, was also held in Belgium with European dignitaries.
On Wednesday, Prince Charles unveiled a memorial in Belgium to the British soldiers who fought and died at Waterloo.
The prince and the Duchess of Cornwall visited the battlefield before unveiling the memorial at Hougoumont Farm, a key site in the fighting.
The site played a crucial role in the victory of the Duke of Wellington's allied army over Napoleon's French forces in 1815, and saw some of the fiercest fighting of the battle.
The memorial depicts two life-size soldiers struggling to close the farm's north gate to save it from being overrun by the French.
Soldiers from the Coldstream Guards managed to shut the gate and Wellington later said the outcome of Waterloo "turned on the closing of the gates at Hougoumont".
Prince Charles and the duchess also took a tour of the battlefield, starting at La Belle Alliance Farm - which served as Napoleon's headquarters.
The duchess has a direct connection with the new monument as her great-great-great-grandfather, John Whitehill Parson, fought at Waterloo while serving with the 10th Regiment of Light Dragoons.
More than 5,000 enthusiasts are due to perform battle re-enactment displays at Waterloo over the weekend as the bicentenary commemorations continue.
And tens of thousands of people are expected to attend a sound-and-light show on the battlefield later.
The battle was fought after French emperor Napoleon conquered large swathes of Europe, before being defeated by allied forces in 1814.
He was exiled to the Mediterranean island of Elba, but escaped the following year, and on 18 June 1815 his troops again faced the combined allied forces at Waterloo - about 10 miles from the Belgian capital, Brussels.
Royal Family members have taken part in a service to commemorate the 200th anniversary of the Battle of Waterloo.