The 19-year-old Paraguay forward unleashed a thunderous, swerving effort into the top right corner from 25 yards seven minutes before the break to mathematically guarantee Albion a sixth-placed finish.
Phil Foden put the newly-crowned champions ahead at the Amex Stadium with his fifth goal in as many starts against the Seagulls.
But, despite bringing back a host of big names, Pep Guardiola saw his formidable side drop points for the first time since February 18 after Erling Haaland's 79th-minute header was disallowed due to VAR spotting a shirt pull on Levi Colwill.
City boss Guardiola was angered by that decision and later shown a yellow card by referee Simon Hooper for his ongoing protestations.
Haaland had wasted two fine first-half chances, while Brighton's Danny Welbeck rattled the crossbar from a free kick and had a goal disallowed for offside, in addition to a Kaoru Mitoma effort being chalked off for handball.
The pulsating encounter was a fitting final home game of an unforgettable campaign for the record-breaking Seagulls and banished the remote chance of them slipping into the Europa Conference League on the final day at seventh-placed Aston Villa.
City were given a guard of honour by their hosts, four days on from securing their fifth title success in six seasons thanks to second-placed Arsenal's defeat at Nottingham Forest.
Haaland - seeking to add to his 36 top-flight goals - should have put City ahead inside six minutes but wastefully headed over.
The visitors were fortunate to survive in the 20th minute when Welbeck's thumping free kick cannoned back off the bar.
Haaland then overran the ball and saw it smothered by Seagulls goalkeeper Jason Steele after being slipped in by Foden before making amends by assisting the 25th-minute opener.
Riyad Mahrez's superb through ball split Albion's defence and Haaland raced clear to draw Steele and square for Foden, who slotted home.
Mitoma saw his bundled finish ruled out and Facundo Buonanotte stung the palms of Stefan Ortega before the eye-catching equaliser arrived.
Enciso collected the ball midway inside opposition territory and advanced to spectacularly lash high into the net from distance, prompting applause from City fans behind the goal.
Former Manchester United forward Welbeck then had a neat finish disallowed for an offside before Foden headed Kevin De Bruyne's cross narrowly over at the end of a breathless first half.
The frantic, end-to-end action extended into the second period, albeit chances were largely at a premium.
Ilkay Gundogan flashed wide and Cole Palmer tested Steele, while Pervis Estupinan's powerful drive flew marginally wide of the left post at the other end.
Treble-chasing City thought they had won it 11 minutes from time when Haaland found space to nod in a cross from substitute Palmer.
But the close-range finish was overturned after VAR review.
