The Blues have agreed to sign the Brazilian full-back and he will join former club-mate Diego Costa at Stamford Bridge once he has completed his medical in London
The Blues have long been linked with a move for the 28-year-old and told Atletico in June that they were willing to pay the €25 million [£20m] release clause in the player's contract, with the player himself telling the Spanish club that he was keen to move to England.
And they have now finalised the move, with Atletico announcing the agreement on Wednesday.
A statement confirmed: "Atletico Madrid and Chelsea have reached an agreement for the transfer of the rights of Luis Filipe, pending [a] medical examination with the English club.
"The Brazilian player had communicated to our club at the end of the campaign his willingness to be incorporated into the London institution."
Filipe Luis will replace Ashley Cole at Stamford Bridge, with the ex-England international having been allowed to leave for Roma on a free transfer following the expiration of his contract.
The left-back will join former club-mate Diego Costa at Stamford Bridge, with the Spain international completing his €44m [£35m] move to the club earlier this week.
Filipe Luis becomes Chelsea's fourth signing of the summer following the arrivals of Costa, Cesc Fabregas and young midfielder Mario Pasalic.