The Manchester United forward was charged following an incident with a fan after a game against Everton in April. He was later cautioned by police and had been charged with a breach of Rule E3.
Kane's brace of goals had enabled England to edge past a gritty Tunisia in its opening match at the FIFA World Cup in Russia.
The appeal was rejected despite FA support as the paperwork was submitted 14 seconds late on deadline day.
The English Football Association has charged Sunderland manager David Moyes for his alleged offensive comments to a female reporter.