clock stoppage

NFL game yesterday. Bills- Steelers. 1:43 left in 4th quarter, Bills ball third down and 4, Steelers out of time outs.Bills run ball up middle for no gain but get a offensive holding call. Clock stops on penalty. Steelers were out of time outs and declined the penalty making it 4th down. I thought after penalty was declined and the ball placed the ref would start the clock. Do you know the rule?