Match referee Mike Procter ruled that England were two overs short of their target at the scheduled finish of the Australia innings on Sunday.
The players were fined five percent of their match fees for every over not bowled in time, and captain Vaughan's punishment was doubled.
England are in real danger of not reaching the semi-finals of the seven-week tournament as they have only two points in the standings with three games to play.
They play Bangladesh at the Kensington Oval in Barbados on Wednesday.
The tournament culminates with the final in Barbados on April 28.
