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"Everybody's here to sing for you tonight, but it's your song that everybody wants to hear,' said the rocker as he invited her on stage.
"This has come as a surprise to me, and a very moving one," said the 67-year-old freedom fighter.
She was presented with Amnesty International's Ambassador of Conscience Award – the rights organisation's most prestigious prize – which she won in 2009 whilst under house arrest in Burma.
The heroine had arrived at a packed Dublin theatre to thunderous applause from a crowd of 2,000 spectators.
A three-hour concert followed featuring songs, poems and speeches in her honor – and a turn from the cast of Riverdance.
The décor – a backdrop of a wall of opened birdcages – depicted her freedom from house arrest in 2010.
Finally came the time for Ms Suu Kyi – known as 'Mother Suu' to her followers – to collect her award, to a standing ovation.
She drew laughs by observing that the British used to consider the Burmese "the Irish of the east", because they never gave the British any peace, both liked a drink and were very superstitious.
Bono flew his guest to the Irish capital from Oslo in his private jet after they took part in a conference of peace mediators together at the end of her four-day visit to Norway.
On Wednesday the politician was due to return to her former home in Britain, where she had lived with husband Michael Aris as a young woman.
Of her return, Ms Suu Kyi said she was "looking forward to rediscovering the places that made me happy".
When she left her home in Oxford to return to Burma her mother was sick, she envisaged being gone for a few weeks.
In the event she didn't return for 24 years, with 15 of those spent under house arrest.
Her sons Alexander, now 39, and Kim, now 34, grew up without their mother.
And sadly her husband died of prostate cancer in 1999 without her by his side. The pro-democracy leader was worried she wouldn't be allowed to re-enter Burma if she travelled to be with him.
Ms Suu Kyi will re-connect with relatives in Oxford during her week long trip to the UK.
She will also address both Houses of Parliament – an honour usually reserved for heads of state – and meet Prince Charles and the Duchess of Cornwall.
And the trip includes a meeting with radio legend Dave Lee Travis, whose programme Jolly Good Show, she used to listen to during her years of house arrest.
It gave her a lifeline, and "made my world more complete", she explained.
All the news as Duchess Kate's due date draws close...