McQueen, who last week moved to the Shrimpers on a loan deal until the end of the season, came off the bench in the 84th minute at Roots Hall.
Southend, who are ninth in the table and just two points shy of the play-offs, led after 24 minutes when Jack Payne struck a low, left-foot shot across goal, just inside the far post.
The hosts doubled their lead seven minutes later when West Ham loanee Stephen Hendrie played in Tyrone Barnett to finish at the near post.
Southend’s hold on the game looked as though it might loosen when they lost midfielder Gary Deegan in the 51st minute to a second yellow card, but they were still able to add a third, as Barnett converted from the spot after Will Atkinson had been brought down by City keeper Reice Charles-Cook.
McQueen was then introduced for Atkinson six minutes from time, with the 20-year-old helping the Shrimpers hold on to a first win in five.
Elsewhere in League 1, Saints winger Lloyd Isgrove helped Barnsley win a fourth successive match, as they further eased any relegation concerns with a 6-1 home win over Rochdale.
Isgrove, who last week extended his stay at Oakwell until the end of the season, started the game and was substituted in the 68th minute.
By that stage, Barnsley led 2-1, with Alfie Mawson’s early header being added to by Sam Winnall’s close-range finish shortly after half-time, before Nathaniel Mendez-Laing nodded in a corner to pull one back for the visitors.
The hosts restored their two-goal advantage in the 69th minute, when Winnall tapped home, and they added a further three in the closing stages, as Marley Watkins fired in a loose ball, before Winnall headed in for his hat-trick and Kevin Long rounded things off.
The Tykes remain 17th in the table and are five points clear of the drop zone.
Two points ahead of them are Swindon Town, with Saints defender Jordan Turnbull featuring as the Robins extend their unbeaten run to three games, with a hard-fought 1-1 draw away to Sheffield United.
United, managed by former Southampton boss Nigel Adkins, led in the eighth minute at Bramall Lane when ex-Saints striker Billy Sharp fired home from the penalty spot, after a combination of Turnbull and Brandon Ormonde-Ottewill were judged to have fouled Paul Coutts in the area.
Town held firm after that, however, and grew into the game, with Turnbull venturing forward and firing a second-half effort off target, before Ormonde-Ottewill cut onto his right foot in the area and finished at the near post in the 79th minute to earn the visitors a point.
In League 2, Jason McCarthy played the full game for Wycombe, as they suffered a 2-0 loss at home to fellow play-off challengers Leyton Orient.
Saints defender McCarthy featured in a more unfamiliar central midfield role at Adams Park, as the Chairboys suffered a third successive league defeat, seeing them drop to ninth in the table, two points off the top seven.
Orient’s goals came via Jay Simpson’s 69th-minute strike, before Calaum Jahraldo-Martin was played in two minutes from time to finish.