The fine was imposed because Frawley was replaced by Matthew Warnock, who had not been named as one of three emergencies for the match.
AFL general manager football operations Adrian Anderson said Melbourne had been fined $10,000 for not using one of its emergency list players, while a suspended sanction of $5000 held over from 2008 for a similar rule breach has been activated.
However, Melbourne general manager of football Chris Connolly said his club had to include Warnock in its final side.
"Our named emergencies on the day did not cover the loss of a key defender. James Frawley was fit to play when the team was selected, and up until the morning of the game," he said.
"Matthew Warnock was at Casey Fields preparing to play for the Scorpions when the decision was made. Fortunately, we were able to get him to the MCG in time to play for the senior side.
"Following this incident, the club plans to recommend to the AFL that the emergency lists be extended to four players, in order to incorporate a back, forward, midfield and ruck player."
The AFL sent a notice to all clubs in April this year reminding them of their obligations around the naming of teams and the replacement of players from the emergency list.
The League said the rules were in place so that no club could gain a tactical advantage over another over the naming of its side for a particular match.
