The Hornets' stand-out performer had given his side the lead in the 13th minute but this was cancelled out by Chris Brown inside two minutes.
Gianfranco Zola's men piled on the pressure in the last half an hour and went close on a number of occasions before James Husband fouled Sean Murray just inside the area and the summer arrival from Nottingham Forest made no mistake from the spot.
The game started at a strong tempo with both sides looking to be positive and it was not a great surprise that it did not take too long for the opening goal to arrive.
And the manner of the opening stages was reflected in McGugan's goal in the 13th minute, with the midfielder driving at the heart of the Rovers backline before lifting the ball over the stranded Ross Turnbull who, despite getting a hand to the ball, was unable to prevent it crossing his line.
Within two minutes though, Doncaster were level and on this occasion it was Turnbull's opposite number Manuel Almunia who was left questioning himself after he could only parry an angled Theo Robinson drive into the path of Brown and he slid the ball home.
Little of the way of goalmouth action then happened until after the half hour mark when Hornets centre-half Joel Ekstrand strode purposefully forward from the back and found Troy Deeney, who released Cristian Battocchio in the penalty area but his attempt to lift it over Turnbull was thwarted by the keeper's legs.
The home side finished the first half the stronger but Brown was not too far away from doubling his tally when he could not quite stretch far enough to convert Husband's low delivery from the left.
The Hornets looked to make the running at the start of the second half but it was Doncaster who had the first two chances, with James Coppinger shooting narrowly over from 30 yards before Brown got up well at the back post to meet a Husband cross but he could not direct his header on target.
It was the introduction of Fernando Forestieri that galvanised the Hornets as a succession of chances came and went.
The substitute's first involvement was to force Turnbull into a save at the foot of his near post before Gabriele Angella saw a goal-bound header from McGugan's corner strike a pile of bodies.
McGugan looked certain to score when Daniel Pudil pulled the ball back to him in the area, only to see Turnbull superbly tip his effort over.
The Doncaster keeper also kept out a stinging Pudil half-volley and Forestieri curled a shot wide, although the hosts were almost caught out when errors from Connor Smith and Lloyd Doyley contributed to new Manchester United loan signing Federico Macheda a clear opening on the left side of the area, but he fired wide.
Ultimately though, Watford's attacking endeavours after the break were to be rewarded as McGugan netted from 12 yards to take his tally for the season to four.