Neil Tennant and Chris Lowe formed the group in 1981, and have since had 22 Top 10 hits and four No.1 singles.
A statement from Ged Doherty, Chairman of the Brits committee said: “Since their first Brit Awards over 20 years ago, Neil and Chris have produced a fantastic body of work with songs that truly were the soundtrack to a whole generation’s lives.
“The Pet Shop Boys have since become one of the most influential groups of the modern era and are deserving recipients of the award.”
Previous winners of the prize include Oasis, Tom Jones, Paul Weller and Sir Paul McCartney.
Earlier this month, it was rumoured that Simon Cowell would be this year’s recipient of the prize.
The 2009 Brit Awards will take place at London’s Earls Court on 18 February.