Raith were made to pay for missing a penalty as two late goals earned Hamilton an away victory.
Following a first half in which goalscoring chances were at a premium, the game sprung to life after the break.
The hosts were awarded a penalty just five minutes into the half after Allan Walker was brought down by Jonathan Page.
Electing to take the spot-kick himself, Walker fired the ball toward the bottom-left corner of the goal, but goalkeeper Kevin Cuthbert did superbly to deny him the opener.
Douglas Hill saw red for serious foul play after 83 minutes and Hamilton took full advantage.
Laurence Ellis turned past his own goalkeeper after 89 minutes and Steven May rubbed salt in the wound by scoring a 25-yard free-kick in the third minute of stoppage time.