Jacob Brown was sent off for a tackle on 34 minutes then Cameron McGeehan, Cauley Woodrow and Jordan Green scored to stretch the unbeaten run to 15 league matches.
The second-placed Reds are still five points behind leaders Luton Town and two clear of third-placed Sunderland who have a game in hand.
Daniel Stendel made one change from the side that drew 0-0 at Portsmouth a week previously, with Kenny Dougall coming in for Mike Bahre.
Southend’s top-scorer Simon Cox had the first chance with a shot from a tight angle on the right of the box straight at Adam Davies then, at the other end, Mamadou Thiam sliced over inside the box after a good move involving Dimitri Cavare, Cauley Woodrow and Brown who crossed low. Thiam also shot wide in the 11th minute with a low 25-yard effort when he should have passed to Cameron McGeehan who would have been clean through on the right of the penalty area.
Woodrow then could not beat goalkeeper Nathan Bishop from eight yards out after attacking full-back Cavare ran onto a good McGeehan pass on the right wing and pulled the ball back.
The red card came when Brown slid in on Sam Mantom with his studs up and, although he only made minimal contact with the Southend player, the referee Kevin Johnson sent him off for the intent and force of the tackle.
Barnsley had created the better chances in a fairly even first half but were even better after the break. The visitors began the second half extremely well, with Lindsay’s header from a McGeehan corner being cleared off the line by a defender. The first goal came on 50 minutes when a throw-in hit McGeehan on the back then fell perfectly for him to turn and fire into the bottom left corner from eight yards out.
Barnsley stayed on top after the goal with Mowatt firing over twice from 25 yards then sending a 15-yard effort narrowly wide of the top left corner after Thiam’s cross fell to him.
The hosts almost levelled in the 72nd minute when Kelman chested down a cross from the left but Davies got down well to his right to save. It was 2-0 a minute later when Southend lost the ball just inside their half and Dougall nudged the ball on to substitute Bahre who played in Woodrow and the striker fired into the bottom left corner from the right of the box 15 yards out for his 14th goal of the season.
Davies again denied Kelman in the 84th minute, diving down to his right to save a weak close range shot by the American who received a pull-back from the left wing. Davies made his best save of the game in injury-time, again getting down to his right to repel Cox’s low volley from ten yards.
It was 3-0 in the 92nd minute when Bahre put McGeehan through on goal and, although his effort was saved by Nathan Bishop, substitute Green tapped into the empty net for his first goal for the club.
Barnsley (4-5-1): Davies; Cavare, Pinnock, Lindsay, Pinillos; Brown, Dougall (76mins), Mowatt, McGeehan, Thiam (Bahre 67mins); Woodrow (Jackson 90). Subs: Walton, Hedges, J Williams, Adeboyejo. Yellow cards: Lindsay. Red cards: Brown. Goals: Woodrow 50, Woodrow 74, Green 90+2.
Southend (4-5-1): Bishop; Bwomono, Turner, Moore, Hart; Kightly (Bunn 62mins), Mantom (Kelman 62), Dieng, Klass, McLaughlin (Yearwood 88); Cox Unused: Smith, Kiernan, Lennon, Hyam.
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