Thursday marks 20 years since the Princess of Wales died in a high speed vehicle crash in Paris while she was with her partner Dodi Al Fayed.
After the garden tour, the princes read cards and messages admirers had left outside the gates of the palace, and the Kensington Palace Twitter account tweeted a message of thanks, saying, "The Duke and Prince Harry are grateful for the many flowers, letters and messages they have received about their Mother".
"The engagement will allow the princes to pay tribute to the life and work of their mother", Kensington Palace said in a statement.
Footage from the visit shows pictures of the princess pinned to the gates, with a growing sea of flowers on the ground.
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Wednesday's walkabout echoed scenes in the immediate aftermath of Diana's death, where a young William and Harry joined their father Prince Charles to see the thousands of tributes left for the Princess of Wales.
This is the fourth Diana memorial in London, with the princess already honoured with the Diana Memorial Fountain in Hyde Park, the Diana Memorial Walk at St James's Palace and the Diana Memorial Playground at Kensington Palace.
William and Harry's appearance had attracted several hundred well-wishers who lined crash barriers and the brothers each placed a floral tribute at the gates for fans of their mother.
More than 12,000 bulbs were planted over the winter to create what is now a breathtaking garden outside the home that William shares with his wife and their two children, Prince George and Princess Charlotte, as well as the cottage where Harry lives.
Her sister added: "A lady gave us the flowers and she said can you give it to one of the princes".
The three royals headed to Kensington Palace's White Garden, which was specially designed as a special tribute to the late princess, in the torrential rain to pay their respects.
They also met with representatives from charities supported by the Princess of Wales.