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Gillingham under-18s were beaten in the first round of the FA Youth Cup despite taking an early lead.
The Gills were ahead after three minutes with a Leroy Hlabi penalty before the visitors levelled things up midway through the opening half.
With no second-half goals, it went to extra-time, where Mayes hit the winner for Portsmouth with a quality finish.
The teams were playing for the right to meet Lewes under-18s in round two, after they progressed through the opening round with a 4-3 win over Camberley Town.
Among the names in Gills’ starting XI was defender Jack Tucker, who played half a game against Portsmouth’s first team in the recent League 1 fixture at Priestfield.
Gillingham made a bright start to the game and went ahead after just three minutes.
Visiting keeper Jack Collins allowed the ball to go through his legs and Hlabi was brought down by Matt Casey, earning the Pompey defender a booking. Hlabi sent the goalie the wrong way from the penalty spot.
The Gills kept the pressure up but it was all-square against the run of play when Dan Smith’s cross was parried by keeper Louie Catherall into the path of striker Matt Mayes, who deflected the ball home, receiving a blow to the face in the process.
That goal spurred the visitors on and made it more of an even contest for the remainder of the half, although Hlabi twice came close to scoring for the Gills again, putting his efforts wide.
Casey, meanwhile, was fortunate to stay on the pitch after a late challenge on Henry Woods. Referee Damith Bandara opted to keep his cards in his pocket to the relief of the already-booked defender.
The start of the second half was a tight affair. Ryan Huckle had an effort saved from a Gills corner and Portsmouth’s Dan Smith had a shot blocked.
Gillingham had appeals for another penalty on 72 minutes, when Miguel Scarlett’s mazy run ended when he went down in the box, but referee Bandara booked him for a dive.
Jack Conway had a shot saved moments later after another run forward had the defence backing off. Portsmouth’s Mayes put a good chance wide after meeting Jack Chandler’s cross at the far post.
Portsmouth sub Oscar Johnston shot narrowly wide just moments after coming on. With no further goals in the 90, the tie went into extra-time.
A frantic few minutes after the restart saw Woods’ powerful effort saved by visiting keeper Collins before Mayes had his effort turned onto the bar at the other end moments later. Lethbridge fired the loose ball wide.
Portsmouth went ahead when Mayes was put through on goal by Johnston and he fired home with 103 minutes gone.
The Gills finished with 10 men when Bandara ordered Woods off. The offence was unclear although it appeared it was for dissent to the official.
Gillingham pushed for an equaliser but Mayes’ goal settled a well contested tie.
Gillingham: Catherall, Scarlett, Arnold, Bramble (Arthurs 84mins), Huckle, Tucker, White, Gildea, Conway (Laing 117mins), Woods, Hlabi. Subs: Walsh, Scheminant, Noyelle.
Portsmouth: Collins, Brooks, Hancott (Flint 106mins), Read, Dandy, Casey, Whiting (Lethbridge 46mins), Chandler (Johnston 83mins), Mayes, Smith, Maloney. Subs: Pitman, Mnoga.