Bute suffered his first defeat at the hands of Froch in May when the Nottingham fighter ripped away his IBF super-middleweight title with a fifth-round stoppage win.
The Canadian is expected to face Froch again in his home country next year and he kept these plans on track by taking a hard-fought verdict with scores of 115-113, 116-112 and 118-112.
Bute, who stepped up to light-heavyweight for this bout, adopted a more cautious approach and did not cut loose until the final round when a sustained attack brought the crowd to their feet.
But he could not shift the tough Russian who fired back stubbornly and Bute had to settle for the decision, handing Grachev his first professional loss.
On the undercard, former world title challenger Allan Green overcame a fourth round knockdown to stop Renan St-Juste, who failed to come out after the seventh.