Cole escaped a ban after he personally apologised to FA chairman David Bernstein.
But this marks the largest ever fine imposed by the FA for a social media-related incident. Cole was also warned as to his future conduct.
In a short statement, the FA said: "Chelsea's Ashley Cole has been fined £90,000 after he admitted an FA charge in relation to a Twitter comment which was improper and/or brought the game into disrepute."
The former Arsenal defender posted the comment after his evidence in the racism trial of fellow footballer John Terry was questioned by the FA.
Terry's defence that he had not racially insulted the QPR defender was branded "improbable, implausible and contrived", and the commission also questioned Cole's statement in support of him.
In response to this, Cole tweeted: "Hahahahaa, well done #fa I lied did I, #BUNCHOFTW*TS."
He deleted the tweet soon after and issued an apology, which read: "I had just finished training and saw the captions on the TV screens in the treatment rooms about what was said in the FA Commission ruling about me.
"I was really upset and tweeted my feelings in the heat of the moment. I apologise unreservedly for my comment about the FA."
Cole's £90,000 fine follows a separate Twitter-related incident in which Rio Ferdinand was fined £45,000 by the FA for appearing to endorse a follower's use of the term "choc ice" in relation to Cole.