Rule 4-3-1

The portion of Rule 4-3-1 pertaining to penalties is the following:

Note: If the game clock was stopped for a foul by either team (whether penalty is accepted or declined), it will be started when the ball is declared ready for play; except when the foul occurred after the two-minute warning of the first half, or the last five minutes of the second half, in which case the clock starts on the snap.

(Source: Official Rules of the NFL.)