Lee, who had earlier given Saints the lead from the spot, was kept out at the second time of asking with six minutes remaining of a tight contest.
After a goalless first half where United created the better of the chances, the hosts went in front with 54 minutes on the watch when Lee was fouled inside the area, but dusted himself down to put Saints into a lead which they looked like holding on to following a stubborn defensive display.
The visitors eventually equalised with ten minutes remaining when Federico Macheda stroked home on the edge of the area, but Lee's squandered chance to take all three points through a second spot kick means that qualification to the Elite stage is now no longer in Saints’ hands.
Saints U21s: Cropper, Young, Stephens, Turnbull, Targett, Reeves, Ward-Prowse, Chambers (Moore 75), Mayuka, Lee, Hoskins. Subs (not used): Johns, Curtis, Sinclair, Forte
Goal: Tadanari Lee (penalty) ‘54
Man Utd U21s: Johnstone, Vermijl, McGinty, Thorpe, Fornasier, Tunnicliffe, Cole, Henriquez (Bebe 70), Macheda (Veseli 90), Petrucci, Lingard. Subs (not used): Pereira, Lawrence, Ekangamene
Goal: Macheda ‘80
United got the game underway defending the Northam stand on a cool night inside St Mary’s, and tried to set the tone with some early, calming possession football across the middle of the park.
It was Saints however, who got the first effort on target, with Emmanuel Mayuka battling his way through into the area to test Sam Johnstone with a fierce low strike, which the ‘keeper pushed away.
The visitors worked their first real opportunity on nine minutes when Angelo Henrique got away down the left side to pick out Federicio Macheda inside the area, but the frontman’s header cleared the top of Cody Cropper’s crossbar.
They went closer five minutes later when full back Sean McGinty drove a cross into the area which clipped the frame of the goal, but with no-one in a white shirt there to follow it in, Saints were able to regroup and clear.
Henrique flashed a header from a Larnell Cole cross wide of Cropper’s right post as they turned the screw, but Saints were still well in the game, with Lee going close to connecting to Young’s deep cross from the right, before Mayuka’s sprint forward earned the home side another corner.
On 23 James Ward-Prowse almost caught United cold with a direct effort from a free-kick on the left, but his whipped strike just dropped wide of the far post with Johnstone scrambling to get across to it.
It was now the turn of Martin Hunter’s men to ramp up the pressure on their opponents, and a smart interchange involving Tadanari Lee and Sam Hoskins saw the latter work the visiting backline with a strong drilled cross into the box.
Saints survived a nervy moment on the half hour when Cropper raced out of his area to intercept McGinty’s through-ball towards Henriquez with the United midfielder nicking the ball passed the American stopper, only for Jordan Turnbull to save the day with a vital block inside the six yard box.
The visitors had an even better chance in their next attack when Jesse Lingard had the whole goal to aim at from a Henriquez cutback, but he fired his effort high and wide of the target.
The last ten minutes of the half belonged to the visitors in terms of possession, but arguably the plaudits should have gone to Saints ‘keeper Cody Cropper, who was at his best to produce a terrific one handed save to deny Henriquez’s rising shot, before diving low to his left to deny Lingard once more with a strong punch away to safety.
He even denied James Ward-Prowse a moment to forget when a deflection off the midfielder towards his own goal was pushed away to safety by the glovesman, as Saints kept the score level going into the break, though Mayuka nearly stole in to snaffle a late goal for the hosts, which was cleared at the second attempt.
Half Time: Saints U21s 0-0 Man Utd U21s
Saints started the second period much brighter and were awarded a free-kick in a dangerous position five minutes into the new half when Calum Chambers was brought down on the edge of the box.
Skipper Ben Reeves struck his direct effort well, but it curled just wide of the left post for a shot that the United ‘keeper would have done well to reach had it gone an inch or two the other side.
But on 54 Saints were awarded a penalty when Tadanari Lee was brought down under a clumsy challenge by Marnick Vermijl inside the area.
The striker stepped up to take the spot kick himself and LEE sent Johnstone the wrong way to find the bottom corner and give the hosts a lead.
The hosts almost doubled their lead moments later, when Reeves bent a superb free-kick onto the roof of the net from 25 yards out, as the chance to add a quick-fire second strike narrowly escaped Martin Hunter’s side.
At the other end, Tom Thorpe headed over the bar from another well worked set piece by the visitors, before United made their first change of the night with Portuguese forward Bebe introduced to the action in place of Henriquez on 70 minutes.
Saints continued to show good attacking intent through Reeves and Mayuka, who linked up well on numerous occasions in the final third, before making their first change when Corby Moore was introduced to the action in place of the hard working Chambers.
United rediscovered their movement in attack, strengthened by the arrival of Bebe and on 77 the substitute put in a perfect cross for Macheda, whose first time strike was parried by Cropper, with the ‘keeper doing well to keep the close range effort out.
Saints’ defensive resolve was finally broken with ten minutes left on the watch. Lingard was initially kept at bay by Cropper, but MACHEDA followed up with a crisp strike that a stranded Saints ‘keeper could do nothing about as United levelled.
Just two minutes later, Saints were awarded their second spot kick of the evening when Lingard was adjudged to have handled the ball in a melee inside the six yard box.
The United midfielder was sent off for his misdemeanour, providing Lee with his second chance from a penalty.
This time though, Johnstone guessed right and kept the Japanese striker’s effort out, as the visitors got out of jail, even if they were a man light for the remainder of the contest.
Frederick Veseli replaced goal scorer Macheda as play entered stoppage time, with neither side able to find a winner.
Full Time: Saints U21s 1-1 Man Utd U21s