A deflected goal early early in the second period was enough to settle this match at Vicarage Road.
Head coaches Chris Cohen and Tom Shaw made five changes, with Callum Elder, Chieo Ogbene, Dan Oyegoke, Freddie Draper and Tom Bayliss all coming into the starting line-up.
The Imps started confidently, creating the first opportunities. Draper did well as early as the third minute when he won the ball twice down the right - his ball looking for Ogbene found its way to Ben House. He could not get his shot away and, although he went down under pressure, the penalty calls did not tempt referee James Bell.
And just three minutes later a diagonal ball from George Wickens found House, who controlled it well and fed Yunus Konak whose powerful shot was blocked.
When the home side did threaten, Bayliss blocked a shot from Hector Kyprianou and Othmane Maamma's cross was high.
Stephy Mavididi threatened with a mazy run down the left, with his shot blocked by Sonny Bradley.
City created more chances as the half progressed, with a number of corners including one which resulted in a Bayliss shot from the edge of the area being blocked.
Ogbene tried his luck from distance after 34 minutes, following a House knock-down, but his shot was always curling away from the goal.
The home side took the lead in the opening minute of the second period, with Mavididi's shot taking a wicked deflection before beating Wickens.
City had to reset and start again. a free-kick, won by House after 52 minutes, provided an opportunity but Coubis' delivery into the area was scrambled away.
A mazy run by Oyegoke after 54 minutes was halted by Kevin Keben, who was booked for his troubles, providing another dangerous set-piece opportunity - from a central position just outside the D. Bayliss' shot was well blocked.
Elerewe did well after a long Bayliss free-kick into the area to pick the ball up and win a corner. Elder's delivery was met by Elerewe whose header came off Ogbene and bounced off the top of the bar.
The Imps made a double change on the hour mark, bringing on Rob Street and Reeco Hackett.
There was a big moment when a Bayliss delivery from the right caused problems, with Street's shot blocked away. Moments later Street again saw a shot blocked from a Bayliss free-kick, this time from the left.
A further attacking change with 20 minutes saw Tom Hamer introduced for his first appearance after suspension. Adam Reach and Dom Jefferies were also sent on, as the Imps prepared to pepper the home area in the closing stages.
There was a frustrating moment when a Hackett delivery from the left fell just behind Street, and he could not connect cleanly with his shot in a dangerous position.
House connected with a low delivery in the first minute of time added on, but in the end the Imps' efforts fell short.
Watford: Ravagua, Keben, Kyprianou, Pollock, Maamma (Mlacic, 70), Boadu (Doumbia, 60), Bola, Bravo (Nabizada, 86), Traore (Diatta, 61), Kayembe, Mavididi (Payero, 70). Subs: Bachmann, Kjerrumgaard, Vata, Zemura.
Imps: Wickens, Coubis, Bayliss (Jefferies, 79), Bradley, House, Elder (Street, 60), Elerewe (Reach, 79), Konak, Ogebene (Hackett, 60), Oyegoke (Hamer, 70), Draper. Subs: Gauci, Towler, Oalafe, Varfolomeev.
Official: James Bell
Attendance: 15,641.
