Duncan had led the club to two top-four finishes in his three previous seasons in charge during his second spell with the Shrimpers, but this time he could celebrate claiming the South-East Conference title with the luxury of Friday afternoon's fixture at Millwall in hand.
This 1-0 win was Blues' fifth straight success, taking their overall tally to 15 wins from 21 League games, and helping the club to reach the fifty-point mark for the campaign. During this time, a 2-0 reverse at Luton Town has been the only blemish.
It had appeared that United were merely going to pick up the one point that would move them nine points ahead of three-time title-winners Queens Park Rangers and all but confirm the silverware's arrival in southeast Essex due to Southend's vastly superior goal difference. Asante's late intervention confirmed that the trophy would be winging its way down the A127.
For long periods of the second-half, Blues' Youths had persistently threatened the Gills' goal in torrid weather conditions without reward but, in the second minute of stoppage time, they launched one last attack.
Duran Reynolds picked up possession on the left-hand side of midfield and advanced down the touchline before swinging a delightful cross into a crowded penalty area. The ball flew to the back post, where a lunging Asante connected with an outstretched boot to direct it into the right-hand corner of the net and promptly threw himself into a spectacular somersault in celebration before his team-mates joined him in a jubilant heap on the sodden turf.
It was another dramatic conclusion to a tough match, with the young Shrimpers emerging victorious in three consecutive games against excellent opposition in the shape of Rushden & Diamonds, Brighton & Hove Albion and Gillingham.
Duncan made just one amendment to the starting line-up against Brighton at the weekend, calling on the experience of Stuart O'Keefe in midfield in place of Marcus Milner, who dropped to the substitutes' bench.
Despite a frenzied opening to proceedings, opportunities to score were few and far between during the first-half. The hosts were first to threaten, Josh Sargeant firing over and Charlie Stimson holding off Reynolds before striking straight at Nathan McDonald in the Southend goal.
It was not until the mid-point of the period that Blues tested Conor Quinn in the Kent club's goal, Medi Abalimba stroking a speculative effort into the 'keeper's gloves. A mix-up in defence almost gave Southend the lead five minutes before half-time as O'Keefe's centre was scrambled out at the near post by a combination of Quinn and defender Connor Essam with Craig Calver lurking.
Gillingham had frustrated Southend during the opening 45 minutes, but the League leaders gradually began to assert themselves after the break, holding onto possession more regularly and attacking the home club in a more incisive nature.
After a Sargeant free-kick had been curled around the right-hand post shortly after the interval for the homesters, the hard-working Harry Crawford powered his way past Callum Davies from Reynolds' pass before crossing into the gloves of Quinn.
A key moment came in the 56th minute when Ade Osifuwa's defensive header dropped into the path of Dean Rance. The midfielder larruped the ball goalwards, but McDonald was equal to the task as he parried out athletically.
On the hour, Crawford was prevented from converting Calver's hooked pass by the legs of Quinn and, in the same move, Abalimba saw his precise finish blocked by a defender.
A sharp passing move led to Crawford searching out Abalimba on the right-hand side but, when Quinn spilled the skilful midfielder's cross, neither the on-rushing Calver nor O'Keefe could find the required finish. Another attack ended in dismay with a quarter-of-an-hour remaining, O'Keefe's effort blocked out and Crawford nodding wide as the ball was turned back into the penalty area.
Calver smashed erratically over the crossbar after Crawford had sent him clear of the last defender and, as the match approached its final ten minutes, it seemed as though the Shrimpers' efforts were in vain. Crawford again tried to find his strike partner, but even when Daniel Rimmer wildly skewed his clearance, it bounced back off of the left-hand upright to safety.
Asante and Milner were introduced to breathe new energy into an impressive display, but it was Gillingham's Liam Geering who had his head in his hands when his deflected 30-yard strike rebounded off of the top of the crossbar with six minutes left.
There was still time for Milner and O'Keefe to exchange passes from distance, the latter's dug-out cross leading to Milner's shot being blocked two minutes from time. However, even as the game entered stoppage time, this Southend United team had belief, and that was rewarded when Asante converted the most important close-range finish of his career.
Though Asante's goal was important, it was only made possible by a fantastic team performance, from McDonald, who has returned despite being released to play a prominent part in goal, to Calver up front with 20 goals this season, via Jamie Dennis, performing heroically in a new position at right-back, and Davis Abbey and Merrick James-Lewis, the engine room of the midfield.
It was day that none of the thirteen players involved, the rest of the squad throughout the season, their parents or Ricky Duncan and his Centre of Excellence staff will ever forget - Southend United U18s: Champions!
Southend United U18s: Nathan McDonald, Jamie Dennis, Adetayo Osifuwa, Duran Reynolds; Medi Abalimba (Marcus Milner 87), Davis Abbey, Merrick James-Lewis, Stuart O'Keefe; Harry Crawford (Kyle Asante 82), Craig Calver.
Substitutes not used: John Owinja, Teddy Nesbitt, Michael Ngoo.