The Lions had the better of the chances in the game, with Heurelho Gomes denying them on several occasions.
A replay was looking a distinct possibility before Morison popped up and slotted Shane Ferguson's cross under the legs of Gomes.
Lions strike bar in opening minute
Watford manager Walter Mazzarri made seven alterations to his side for the Hornets trip to the league one play off places.
Lee Gregory almost gave the South London side the perfect start after latching on to an excellent Aiden O’Brien cross but he could only divert the ball on to the crossbar after just 17 seconds
The tie gradually settled down but there was little or no threat from the Premier League outfit as they failed to muster a single shot on target during the first half at The Den.
Gregory was heavily involved in a first period that was largely contested in the middle of the park. There were a few feisty challenges although referee Martin Atkinson only produced three yellow cards all afternoon.
Hornets' 'keeper struck down with injury
Watford keeper Costel Pantilimon was forced off with a knee injury after a heavy but fair tackle from Gregory that forced the Romanian international off the pitch. Gregory then forced substitute Gomes into a very smart save.
For Watford’s part, only an Adeline Guedioura shot that fell well wide of the post without troubling Lions keeper Jordan Archer signalled any intent.
A strong penalty appeal for an apparently blatant trip on Jerome Sinclair angered Mazzarri but left Atkinson unmoved. Even though replays clearly show that he Hornets should have had a spot kick.
Gomes keeps Watford level
Morison produced another smart save from Gomes as Neil Harris would have been the happier of the two manages with the effort his players were putting in.
Watford were having more prolonged periods of possession in the second period but it still looked as if a set piece would be their best way to goal.
A slight concussion for defender Brice Dja Djedje added to Mazarri’s injury worries as he suffered a minor concussion and was replaced by Daryl Janmaatt.
Morison strikes late in game
The key moment arrived in the 85th minute of the tie when substitute full back Ferguson burst down the left and sent in a wonderfully accurate cross which Morrison swept past Gomes on the half volley
Hornets skipper Troy Deeney came on as a late substitute and finally got the first shot on target for his team with a weak backward header from a corner which was comfortably saved by Archer.
Morrison thought he’d capped off a fine performance to seal the cup tie in stoppge time but his effort was rightly ruled out for haandball.
Despite six minutes of added time Watford could not find a way through and Millwall held on to deservedly book their place in the fifth round draw on Monday night.