The Hornets had led 2-0 at Vicarage Road with Javier Acuna and Davide Faraoni both scoring well-taken individual strikes either side of half-time to put the Championship outfit on the verge a minor upset.
But the visitors hit back with 15 minutes remaining as Josh Murphy continued the trend of scoring fantastic efforts with Hooper then equalising for Chris Hughton's side with the last touch of normal time.
The summer signing from Celtic then scored the winning goal of the game as he coolly finished when through on goal with just five minutes of extra time remaining.
Gaston Ramirez has rarely looked like a £12million player since joining Southampton but gave a glimpse of his undoubted quality in their unconvincing 2-0 League Cup victory against Bristol City.
Signed to much fanfare last summer, the 22-year-old has impressed only fleetingly since swapping Bologna for St Mary's.
Having netted in the 5-1 win at Barnsley in the second round, the Uruguayan hammered home a sumptuous volley to put Saints ahead after 15 minutes.
Playing with style and swagger, Ramirez came close twice more in the first half and continued to prove a handful after the restart.
Jos Hooiveld's powerful header seven minutes from time ended City's hopes of winning their first third-round tie in a decade - a match Saints ended with 10 men after Ramirez hobbled off in stoppage time.
Two late goals denied Derby a first win in Leicester for over a decade as the Foxes came from behind to reach the fourth round with a 2-1 triumph.
The Rams were the better side for the majority of the match and comfortably led through Chris Martin's first-half goal.
A first triumph on Leicester soil since a 3-0 success at Filbert Street in February 2002, when this was a Premier League fixture, looked firmly on the cards - until the introduction of Anthony Knockaert.
The Foxes substitute equalised with a stunning free-kick after 78 minutes and then had a hand in Danny Drinkwater's winning goal just three minutes later.
Danny Ings claimed another Turf Moor brace to clinch Burnley's progress with a 2-1 win at the expense of Nottingham Forest.
The visitors had taken the lead in the all-Championship affair when Matt Derbyshire claimed a typical poacher's goal.
However, the Clarets always pose a threat with striker Ings in such blistering form and he struck in each half to take his tally to nine for the season, and four in this competition, to send Burnley through.
Nick Proschwitz grabbed his first goal of the season as Hull edged past Huddersfield 1-0 in a battle of the second strings at the KC Stadium.
The result earned Steve Bruce's side a place in the fourth round but the lethargic nature of the match, coupled with a total of 19 changes across both starting XIs, suggested it was a prize neither were overly concerned about.
Proschwitz, looking to win a place in Bruce's plans for the Barclays Premier League, rifled home in the 59th minute but was otherwise an uninspiring presence in attack and missed a glorious opportunity to double his tally following a misplaced pass by goalkeeper Alex Smithies.
Yet the German forward scored four times in a reserve team outing last week and showed his poaching instincts were still alive when he met George Boyd's cross eight yards out with a powerful finish.