City accepted the charge on Friday, which stemmed from the 50th minute award of a penalty which James Milner converted to help Liverpool earn a 1-1 draw at the Etihad Stadium on March 19.
Gael Clichy was penalised for a high boot on Roberto Firmino and City's players surrounded referee Michael Oliver.
A statement from the FA read: "Following an independent regulatory commission hearing, Manchester City have been fined £35,000 after the club admitted an FA misconduct charge
"City breached FA Rule E20(a) in that in or around the 50th minute of the game against Liverpool on 19 March 2017, the club failed to ensure that its players conducted themselves in an orderly fashion."
Sergio Aguero would earn City a point with an equaliser 21 minutes from time.
City were also fined £35,000 earlier this season for a similar offence during an ill-tempered clash with Chelsea on December 3.