The teams were all square deep into the second half of extra-time when Charles’ 116th-minute curling cross from the right crept past a couple of defenders and deflected in off the inside of the post.
South coast side Southampton, relegated from the Premier League last season, are now set to face Hull, 2-0 winners over Millwall on Monday, for the chance to join already-promoted Coventry and Ipswich in English football’s lucrative top-flight.
The tie, however, has been overshadowed by allegations Southampton, now on a 20-game unbeaten run in the Championship, spied on a Middlesbrough training session ahead of Saturday’s goalless first leg at the Riverside Stadium.
The English Football League charged Southampton after receiving a complaint from Middlesbrough “relating to alleged unauthorised filming on private property” and it remains to be seen what action, if any, officials will take against the Saints.
But should Tuesday’s result stand, Southampton will be through to their second Wembley appearance of the campaign, following an FA Cup semi-final defeat by Manchester City last month.
“A big advert for the Championship, an outstanding game,” Southampton manager Tonda Eckert told Sky Sports.
Eckert, asked about the possibility Saints could be thrown out of the play-off final following the EFL probe into the ‘spying’ charges, replied: “We’ve had this topic the last game as well. There is an ongoing investigation and the club has made a statement.
“We will do everything we can to prepare for the game coming up.”
Following the first leg, Middlesbrough boss Kim Hellberg accused Southampton of trying to cheat.
But after Tuesday’s match the “proud” Hellberg was non-committal about the prospect of his side getting a reprieve.
“We had a plan if we won the game and now we haven’t so now I’m disappointed,” he said.
“Congratulations to the players and the supporters of Southampton for the winner.”
Riley McGree put northeast side Boro ahead in just the fifth minute at St Mary’s when he shot low beyond Saints goalkeeper Daniel Peretz.
Tempers frayed, with Boro defender Luke Ayling reportedly accusing Southampton’s Taylor Harwood-Bellis of using “discriminatory language”.
Hellberg and Eckert then had to be physically separated as referee Andy Madley spoke to them on the touchline towards the end of the first half.
But Southampton, who finished fourth in the table to Middlesbrough’s fifth place, equalised in stoppage-time when Ross Stewart nodded in a rebound after Ryan Manning’s shot was parried into the air by Boro keeper Sol Brynn.
Brynn blocked a shot from Saints substitute Cyle Larin in added-on time after the end of 90 minutes before Charles had the last word. (AFP)