Mike Williamson headed Watford in front in the first period of extra time before Scott Severin scored in the 120th minute to put the tie beyond doubt.
Barnet gave the Hortnets a good game and created several chances but Richard Lee in the Watford goal made a fine save late on to keep the game at 0 - 0 and to force extra time.
Thankfully for Watford they came through the tie and into round 2.