Speaking at a news conference in the German capital, the 54-year-old Sir Simon said he would sign the extension of his contract in September after the Berlin city-state legislature formally approves the decision along with a pact on public subsidies for the orchestra.
His contract would normally have run out in 2012.
"We are thrilled about working with him for the nine years to come," the chairman of the orchestra's board, Andreas Wittmann, told reporters.
The orchestra's musicians expressed the wish one year ago for Rattle to stay on following speculation they wanted to oust him. The 128 members of the orchestra have the right to veto the appointment of their chief conductor.
Rattle has been quoted as describing his relationship with the orchestra's musicians as "turbulent" but he is extremely popular with Berlin's passionate music lovers and his concerts are routinely sold out.
He arrived in Berlin from Birmingham in 2002 and succeeded Italian maestro Claudio Abbado.