The EPL club were initially given a suspended six-point deduction along with the fine but the points penalty has now been replaced by the suspended transfer ban.
The FA confirmed the imposition of sanctions on the west London club on Friday, who admitted to 74 breaches in total of FA regulations covering agents, working with intermediaries and third party investment in players.
Chelsea's new owners self-reported the breaches to the football authorities in 2022, when they were in the process of buying the club from Russian billionaire Roman Abramovich.
The six-point deduction, suspended until June 30, 2027 was imposed by the independent commission which initially heard the case but the club appealed. An appeal board instead replaced the points penalty with the suspended two-window transfer ban.
Chelsea have previously entered sanction settlements in regard to the matter with the Premier League and UEFA.
Chelsea issued a statement saying: "In 2022, the club self-reported potential historical rule breaches to all applicable regulators. Following that report, it has worked openly and transparently with all regulators, including voluntarily and proactively disclosing many thousands of documents."
The club said they were "pleased to confirm that, now the FA process has concluded, this brings all regulatory proceedings against the club to a close".
The written reasons from the original independent commission, which heard the case on December 8 last year, confirmed the 74 FA charges related to 44 transactions involving 32 players between July 2009 and August 2022.
That commission's findings criticised the "breathtaking disregard" for the rules shown by senior executives at the club at the time.
Meanwhile Chelsea winger Mykhailo Mudryk has been cleared to "return to competition with immediate effect" after anti-doping disciplinary proceedings were resolved, the Football Association have announced.
