Virgo fired a low drive from 30 yards through the Coventry wall after substitute Patrick Suffo had needlessly conceded a free-kick. It was a repeat of Virgo's late rescue act for Brighton from the Division Two play-offs last season.
Brighton were behind to Swindon in the semi-finals when Virgo equalised at the end of extra time and he then scored one of the penalties in the shootout, before helping the Seagulls to beat Bristol City in the final.
Virgo's point saver was no more then Mark McGhee's young side deserved, after falling behind in the 69th minute to a sweet strike Stephen Hughes.
The former Arsenal prospect, trying to rebuild his career after unhappy spells at Everton, Charlton and Watford, pounced with a right-foot volley from inside the area which gave Brighton's Dutch keeper Michels Kuipers no chance.
Kuipers kept Brighton's hopes alive after that with fine signs from Lewis Carey and Bjarni Gudjonsson - before Virgo's late show.
Brighton, with 17-year-old Jake Robinson making his first start in the league, had the best of the chances in a bright first half. Summer signings Darren Currie, Maheta Molango and Albert Jarrett all went close to putting them ahead.
Coventry's main threat came from Graham Barrett, who had an extended loan with Brighton when they were relegated from Division One two seasons ago. The Republic of Ireland international had a back-heel from close range smothered by Kuipers.