The Dublin four-piece have heavily campaigned for her release for the last nine years and even penned the Grammy award winning single 'Walk On', taken from their 2000 album 'All That You Can't Leave Behind', in her name.
Ms Suu Kyi won the Burmese elections in 1990 with the National League for Democracy but was never allowed to take power and has been under house arrest ever since.
She was due to be freed but her sentence was extended for a further 18 months last week when she let a US national, John Yettaw, into her lakeside home after he swam there uninvited, preventing her from taking part in elections scheduled for 2010.
U2 singer Bono told a crowd of 88,000 at Wembley Stadium during the second night of their 360° Tour of the UK: "An extradordinary woman has spent 20 years under house arrest. Her only crime is if she had run for election she would won have that election.
"Her name is Aung San Suu Kyi. I send a prayer from London to Burma for her safety."
The frontman then urged the crowd to don masks of the pro-democracy leader, which were handed out during the gig, as the band launched into 'Walk On' while volunteers marched onstage with her face on.
The band played a mammoth two hour set under their giant 'claw' stage as they blasted through a host of their greatest hits plus seven tracks from their recent album 'No Line On The Horizon' including an elecro version of 'I'll Go Crazy If I Don't Go Crazy Tonight'.
U2 also revisited some old classics including 'The Unforgettable Fire', which has only recently been showcased on their world tour for the first time in over 20 years, and 'Ultraviolet (Light My Way)' which saw Bono firing off red laser beams from his jacket while he swang across the stage on a circular microphone.
Later the whole stadium also belted out the words to fan favourites 'I Still Haven't Found What I'm Looking For' and 'Pride (In The Name Of Love)' while the likes of Led Zeppelin's Jimmy Page, Hollywood actor Kevin Spacey and Mel C watched the show from the sidelines.
Bono was on jovial form throughout the show often throwing in snatches of tracks by The Rolling Stones, Frankie Goes To Hollywood, The Beatles, Led Zeppelin and Black Grape mid-song.
He also paid tribute to the city of London on numerous occasions and joked: "If you want our claw for the Olympic Games we'll give you a good deal when the tour finishes."
The band rounded off the show with a poignant rendition of 'One' before Bono urged the crowd to lift up their mobile phones and light up the stadium for closing track 'Moment Of Surrender.
'No Line On The Horizon'
'Get On Your Boots'
'Until The End Of The World'
'New Year's Day'
'I Still Haven't Found What I'm Looking For'
'The Unforgettable Fire'
'City Of Blinding Lights'
'I'll Go Crazy If I Don't Go Crazy Tonight (Remix)'
'Sunday Bloody Sunday'
'Pride (In The Name of Love)'
'Where The Streets Have No Name'
'Ultraviolet (Light My Way)'
'With Or Without You'
'Moment of Surrender'