Time Outs

• One of the primary ways in which players or coaches themselves can stop the clock in a National Football League game is by calling a time out. Each team gets three time outs in the first half, three time outs in the second half and two more during the overtime period, when applicable. Time outs typically last either 40 seconds or, in the case of a television commercial break, 1 minute 50 seconds. Referees can call an official time out at any time, and additional time outs are allowed in the case of injuries.
  
  

Out of Bounds

• Each football quarter lasts 15 minutes, and in the last two minutes of the second and fourth quarters, players can stop the clock by running out of bounds. At all other times during the game, time continues to tick away, even if a player runs out of bounds. This allows teams to attempt last-minute scoring drives at the end of each half, while also shortening the game at nonessential moments.
  
  

Incomplete Passes / Spiking the Ball

• Furthermore, according to NFL Rules regarding clock stoppage, the clock stops every time a quarterback (QB) throws an incomplete pass. This allows for a QB to throw a ball away during a drive to save a few precious seconds, or spike the ball into the ground to force a stoppage of play. Of course, in both cases, a down is expended in the process.
  
  

Challenging a Play

• The clock also stops any time either team's coach challenges a play on the field, or when the booth officials order an instant replay. For a coach to challenge a play, however, he must have at least one of his challenges remaining and must still be in possession of a time out.
  
  

Change of Possession

• The clock is stopped after all changes of possession, whether a turnover, a punt, a kickoff, etc. According to NFL rules regarding clock stoppage, the clock is restarted after the first snap taken by the team now in possession of the football.
  
  

Penalties

• Finally, that brings us to clock-stoppage rules and penalties. According to NFL.com, "With the exception of the last two minutes of the first half and the last five minutes of the second half, the game clock will be restarted... after declined penalties when appropriate on the referee's signal."