Richarlison, who joined Tottenham from Everton last week for a reported fee of £50 million plus up to 10 million in add-ons, threw the flare after his goal in Everton's 1-0 Premier League win over Chelsea at Goodison Park in May.
The 25-year-old celebrated his 46th-minute goal by picking up the flare, which had landed on the field, and throwing it back towards the stand.
The FA said in a statement on Tuesday that Richarlison admitted his conduct was improper and that he had been fined £25 000 for the incident.
Brazil forward Richarlison, who scored 53 goals for Everton, has joined Tottenham in a deal reported to be worth an initial £50 million.
The north London club begin their Premier League season with a home match against Southampton on 6 August.