An earlier independent commission had imposed a suspended six-point deduction, which was set aside and the suspended transfer ban was imposed in its place.
The club had admitted to 74 breaches of FA regulations covering agents, working with intermediaries and third-party investment in players.
Chelsea's new owners self-reported the breaches to 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 that initially heard the case but the club appealed against that.
An appeal board instead replaced the points penalty with the suspended two-window transfer ban.
"The FA charged Chelsea FC with 74 breaches of FA Rule E1.2 after its current ownership self-reported misconduct upon its purchase of the club. The FA is continuing to investigate individual misconduct arising out of this case," the FA said in a statement.
"Chelsea FC admitted to the 74 breaches of FA Rule E1.2 prior to a hearing and an independent Regulatory Commission imposed a six-point deduction, which was to be suspended until 30 June 2027, and a £10 million fine.
"The club appealed against the suspended points deduction and an independent Appeal Board allowed the appeal and set aside this sanction following a further hearing. In its place, the Appeal Board imposed a registration ban for two complete and consecutive transfer windows which is suspended until 30 June 2027.
"The £10 million fine imposed by the Regulatory Commission was not subject to appeal and the full amount will be invested into grassroots football."