"However, to be in this situation is really not up to standard."
Kerrin McEvoy, who rode the race winner Cross Counter, was fined A$3000 ($3248) for also exceeding the whip limit, using it nine times before the final 100m.
So too was Michael Walker on third placegetter A Prince of Arran, meaning all of the top three finishers breached the rules, along with three other riders in the race.
Bowman rode Cheval Grand to victory in last year's Japan Cup, but he will be forced to sit it out this year if he can't successfully challenge the ban.
It also cost him the chance to ride Brave Smash and Latrobe in Group One races on Thursday's Oaks meeting.
The fines of the jockeys for excessive whip use would add to the anger of animal rights activists who were outraged by the euthanising of The Cliffsofmoher, which shattered a shoulder bone early in the race.
Race favourite Yucatan and Bowman's mount Marmelo were reported as being lame after the race, Avilius suffered lacerations when colliding with Thecliffsofmoher as it shifted suddenly due to its injury, and Magic Circle - which was heavily backed in betting markets - suffered internal bleeding and finished near the rear of the field.
Bowman has become a household name for his long association with Winx, taking over the ride on the mighty mare permanently in 2015 and steering her to each of her four Cox Plate victories.