Praising the survivors for their bravery, the duke told them: “We think you are very strong and very brave, you’ve made amazing progress.”
The couple’s official two-day visit began on Friday, and is seen as a mission to promote British interests.
They also visited the Musee d’Orsay and saw France v Wales in the Six Nations.
Some 90 people were killed by gunmen at the Bataclan music venue in Paris in November 2015. Another 40 people died in attacks elsewhere in the city on the same night.
The royal couple met a 25-year-old, called Jessica, who was shot seven times in the leg, hip and back as she dined with friends on her birthday at La Belle Equipe restaurant, and Kevin, 28, a Bataclan concert-goer shot in the leg.
Jessica, whose friend Victor Munoz was killed with one shot, said: “At first I was a bit shy and didn’t want to talk about it because of all of the pain and grief.
“But now I want to say we are not only victims, we have lives, we have boyfriends, girlfriends, work.
“I want to speak about my friend who died, to honour him. I want people to remember who he was.”
As the duke and duchess toured the historic Les Invalides hospital, where they also met war veterans, a man was shot dead as he tried to grab a soldier’s gun attack at Orly Airport in Paris.
The incident did not affect their itinerary and there was no sign of security being increased.
They later attended a “Les Voisins [neighbours] in Action” event at the Trocadero square, highlighting the ties between young people in France and the UK, before moving on to the rugby at the Stade de France.
France scored a try and a conversion to win 20-18 over Wales deep into extra time.
Not since the Queen’s visit to the Republic of Ireland in 2011 have the royals had such a clear-cut foreign mission.
Not that the British government would ever admit as much, but it is that same government which decides where to deploy the senior royals on their foreign travels – and at the moment the royals are being despatched to countries within the European Union.
Prince William and Catherine in Paris over the past two days and then, in July, to Germany and Poland; Charles and Camilla to Italy and Austria in a couple of weeks; and not forgetting that the Queen herself will be hosting a state visit to Britain by the King of Spain in June.
The British Royal Family are expected to be strictly non-political at home – but on their official foreign travels they are emblems of Britain and instruments of British foreign policy.
And right at the moment – with hugely important and potentially very difficult Brexit talks about to start – they are being sent off in pursuit of British interests.
They are, perhaps uniquely, able to represent the bigger picture by drawing attention to the many shared interests the United Kingdom has with its European neighbours – interests and endeavours which will continue long after the ink has dried on whatever terms the politicians finally agree for Britain’s withdrawal from the European Union
Speaking at the start of the official visit on Friday, the prince said the UK’s relationship with France would continue despite the vote to leave the EU.
He said the friendship and co-operation between the two nations “would not change”.
It is Prince William’s first official visit to the city where his mother, Diana, Princess of Wales, was killed in a car crash in 1997.
The trip comes also comes after the duke faced questions over his work ethic for missing a Commonwealth celebration to take a skiing holiday with friends.
It led to criticism from some newspapers after a video emerged of him dancing and in a DJ booth during the trip
The couple have travelled without their children, three-year-old George and one-year-old Charlotte.
Kensington Palace said the trip was at the request of the Foreign and Commonwealth Office.
A spokeswoman for the Foreign Office said: “Royal visits play a very important role in the United Kingdom’s bilateral diplomacy.
“Whilst every royal visit is unique, each visit is designed to support foreign policy objectives and promote closer ties across a range of areas, for example cultural, economic or political, between the UK and the host country.”