The penalty incident came in the 76th minute of an end-to-end match in which the home side will find it difficult to believe they didn't score.
It proved to be something of a smash and grab raid by the second string, who sealed the match when Johnnie Jackson weaved into the Watford area and was dragged down by home goalkeeper Richard Lee. Clemence made no mistake from the spot.
Gary Doherty started his second game following his return from injury, while Clemence began his fourth.
Doc lined up in defence alongside Alton Thelwell, James Quilter and Maurizio Consorti - playing in a slightly advanced role. Clem was joined in midfield by Oyvind Leonhardsen, making his return after a calf injury, George Snee and Jackson.
Steven Ferguson, another returning after a lay-off, and Yannick Kamanan provided the spearhead.
The game had an open feel to it right from the very beginning and there could have been six or more goals in the opening 20 minutes.
The home side started the brightest and Leonhardsen conceded a free-kick on the edge of the area that was whipped in by David Noble. His shot came out off the underside of the bar, hit keeper Hirschfeld and span out of play.
The trialist keeper, playing his second reserve game, then reacted smartly to save a snapshot volley from former Newcastle man Stephen Glass.
Spurs began to make an imprint on the game and a Leo cross caused great confusion between Watford keeper Richard Lee and his defenders. Kamanan then had a shot on the run that drifted just wide.
Dutchman Nordin Wooter then missed his first opportunity of the game, blasting over the bar when neatly set up by Dominic Foley. Jason Norville seconds later dragged an effort across goal.
On 20 minutes Watford perhaps had the best opening to take the lead when Kamanan was dispossessed retrieving a ball approaching the edge of his own area and Wooter was gifted a free shot at goal that was well blocked by Hirschfeld.
In the next movement of the game Ferguson burst clear, took aim, and curled his shot onto Lee's left hand post.
A Noble dipper just saved and a Wooter volley when well placed again were other chances spurned by a tigerish Watford side, while Ferguson went close for Spurs after being set up following a dash down the left flank by Kamanan.
Clemence forced Lee into a fine low save before Watford went up the other end and Norville forced Hirschfeld into making a similar stop. From the resulting corner Hirschfeld produced a spectacular high diving save to deny Norville again.
Hirschfeld was called into action again right at the beginning of the second period, Foley unleashed a shot on the turn from about eight yards out and the Canadian somehow got fingertips to it to divert the effort over.
Minutes later he made a slight error of judgement from a Noble cross, but Jackson was on hand to clear off the line.
Spurs managed to string together a significant period of possession in midfield, something made difficult all night by Watford being so quick to close down and narrow the options. From this passage of play Leonhardsen went close with a half-chance from the right hand side of the area.
With ten minutes gone in the second half, Colin introduced under-17 youngster Mark Yeates for his reserve team debut to replace Leonhardsen. He appeared to be taking up an advanced position with Kamanan drifting out wide. With his first touch he very nearly played Ferguson in on goal.
On 70 minutes he was joined by his under-17 team-mate Jonathan Black, who entered the fray in place of Ferguson. He slotted in on the left side and Kamanan returned to a forward position.
From the corner that caused the break in play that allowed him to come on, Clemence floated in and Kamanan came very close to opening the scoring with a bullet header that was saved at point-blank range by Lee.
On 76 minutes Jackson picked up the ball on the edge of the area and dribbled past the two central defenders before being hauled down by keeper Lee. Referee Mr Friend pointed to the spot straight away and Clemence cooly slotted his kick home low to Lee's right. A rare goal from Mr Clemence...
With minutes remaining Hirschfeld again saved smartly, this time from sub Elliott Godfrey - it was not to be Watford's night.
Team: Hirschfeld, Consorti (Perry 87), Doherty, Thelwell (C), Quilter, Clemence, Snee, Leonhardsen (Yeates 55), Ferguson (Black 70), Jackson, Kamanan. Subs: Jalal (GK), Foster, Perry.
Watford: Lee, Neill (C), Gibbs (Forde 71), Swonnell, Issa, Ifil, Wooter, Noble, Foley, Norville (Godfrey 75), Glass (Wright 45). Subs: Watson (GK), Mawer.
A Stephen Clemence penalty sealed a 1-0 win for our reserves against a tenacious Watford side at Vicarage Road on Tuesday night.