Gutsy Pompey’s hearts were broken nine minutes from time as Manchester City left it late to claim victory.
Mikey Harris’ side appeared to be taking the FA Youth Cup tie into extra-time after a full-blooded and fearless display against the Premier League giants.
Harvey Bradbury had levelled for the Academy on 70 minutes by turning home the energetic Jez Bedford’s cross, leaving the fixture poised at 1-1.
The substitute, whose dad Lee once played for City as well as Pompey, sparked celebrations among the impressive 1,779 Fratton Park crowd which had braved awful conditions and traffic problems to attend.
But with thoughts of an improbable upset against City, Brahim Diaz struck with a fine individual goal on 81 minutes.
Aged 16, the Spaniard joined for £300,000 from Malaga in 2013 and was a threat throughout.
But until his intervention, Jason Wilcox’s side could not add to Lukas Nmecha’s 13th-minute opener.
They were thwarted by a magnificent showing from Pompey, who were not overawed by the occasion and can be rightly proud of their performance.
Fittingly, those present gave a standing ovation to the home-grown youngsters of which surely some which find themselves in the first-team in the future.
Nonetheless, Diaz had the final say with his sublime late strike.
However, every single member of Pompey’s squad showed their worth in a 2-1 defeat which enhanced many a reputation out on the Fratton Park turf.
The match was delayed by 30 minutes because of traffic problems around the city on a wet and windy night.
When the fixture did kick off, a timely slide challenge by Ousman Saidy dispossessed Nmecha inside the box on eight minutes as he shaped up to shoot.
At the other end, Bedford tried his luck from long distance with a right-foot shot which flew wide of the target.
However, the deadlock was broken by the visitors on 13 minutes following a slick move from the right.
Rodney Kongolo slipped the ball inside to Nmecha who, with lightning reactions, crashed a right-foot shot into the net a split second before the tackles arrived.
City should have doubled their advantage three minutes later when Javairo Dilrosun crossed from the left and Diaz somehow shot wide at the far post.
Pompey were having their moments, though, and Kaleem Haitham and Brandon Joseph-Buadi posed problems in one attack, with the latter then feeding Bedford.
However, the forward was squeezed well by the City defence and his subsequent shot blocked from the angle.
Blues keeper Alex Bass then made two tremendous stops to come to his side’s rescue.
In the 27th minute he flung himself to his left to brilliantly keep out Kongolo’s curling shot from the right.
Then he bravely dived at the feet of Nmecha as the striker burst into the penalty area, conceding a corner in the process.
Harris’ side were finding their feet, though, and beginning to pose a greater threat to the visitors’ Milton end goal.
Sure enough, on 36 minutes it took a superb stop from Daniel Grimshaw to keep the scorelines level as the Blues grew into the game.
Impressive Blues skipper Calvin Davies pulled the ball back from the right and Bedford’s fierce shot was pushed over by the City goalkeeper.
The teams entered the interval separated by just the one goal, providing Pompey with still enough opportunity to find a way back into the game after the break.
After the restart, Bass was again called into action when Nmecha’s shot took a deflection off Kyle McDowell and, from point-blank range, the Blues’ keeper produced a superb juggling stop.
On 56 minutes delightful play down the left from Diaz saw him wrongfoot Theo Widdrington only to drive his effort wide of the far post when he should have done better.
Referee Graham Kane awarded the visitors a penalty on 66 minutes after Bass took out the powerful Nmecha as he charged into the box.
However, linesman David Ellis intervened – with the Blues players and subsequently Kane noticing his raised flag in recognition of offside.
Minutes later City went one further and had the ball in the net through Nmecha but once again the linesman, situated in front of the South Stand, called for offside.
Yet it was all level on 70 minutes and how Fratton Park celebrated.
Bedford instigated the equaliser, surging down the left and pulling back a cross which was steered into the bottom corner by the right foot of Bradbury.
Pompey had the momentum and Bedford then showed a clever piece of skill before firing in a shot which was deflected for a right-wing corner.
With the atmosphere cranked up, it was proving to be an exciting end to the fixture and Bass had to collect Dilrosun’s shot from outside the area, dealing with it without too much trouble.
Then on 81 minutes the visitors restored their advantage when Diaz burst through the centre of the defence and calmly finished.
The bright Bedford’s response was a fierce shot from long range which Grimshaw had to gather at the second opportunity.
The was to be no coming back for a second time from the hosts, however, and City ran out winners on a night the Blues youngsters can be so proud of their display.
Pompey: Alex Bass, Calvin Davies, Ousman Saidy, Theo Widdrington, Kyle McDowell (Tommy Scutt, 87min), Adam May, Alex Oxlade-Chamberlain, Kaleem Haitham, Jez Bedford (Sam Woodward, 87min), Brandon Joseph-Buadi, Liam Sayers (Harvey Bradbury, 57min). Subs not used: Nick Hall, Dan Smith
Manchester City: Daniel Grimshaw, Demeaco Duhaney, Charles Oliver, Tosin Adarabioyo, Jacob Davenport, Marcus Wood, Aaron Nemane, Rodney Kongolo, Lukas Nmecha, Braham Diaz, Javairo Dilrosun (Isaac Buckley-Ricketts, 84min). Subs not used: Christian Kjetil Haug, Cameron Humphreys-Grant, Ayotomiwa Dele-Bashiru, Paolo Ferndandes-Cantin