The Tykes played almost an hour with a man disadvantage after Jacob Brown’s red card at Roots Hall.
But goals from Cameron McGeehan, Cauley Woodrow and Jordan Green after the break kept the club’s promotion challenge on track.
Following their 20th league win of the campaign, Stendel’s side remain two points above third-placed Sunderland, who have a game in hand.
The German said: “It was a test for our mentality and I think we passed it.
“The kick for our team was the red card.
“At half-time we told the players they had to work hard together and they played with a lot of heart.
“From my position I was very surprised he got the red card.”
Victory extended the Tykes’ impressive unbeaten run to 15 games and they have not conceded for three games. They remain five points behind Luton Town, who enjoyed a 2-0 home win over Rochdale while Sunderland defeated Plymouth Argyle 2-0.
Stendel’s charges started the game brightly with Mamadou Thiam hitting two efforts off target.
Former Fulham striker Woodrow was well kept out by Nathan Bishop from Dmitri Cavare’s pull-back.
Brown was sent off 10 minutes before the break for a knee-high tackle on Sam Mantom after losing control of the ball in the centre circle.
But being a man down did not dampen the Tykes’ threat.
McGeehan fired home his fifth goal of the season just five minutes after the restart, turning swiftly to net after a long ball had struck him on the back of the neck.
Alex Mowatt almost doubled the lead minutes later, but he lashed the ball narrowly over the bar.
Southend responded and Reds goalkeeper Adam Davies produced a fine stop to deny Charlie Kelman and keep the visitors in front.
Woodrow instantly made the hosts pay down the other end as he slotted the ball into the bottom corner.
It was Woodrow’s 14th goal in 25 appearances and underlined just how important he will be to the Reds’ cause with target man Kieffer Moore having been ruled out for the rest of the season on medical advice after a head injury.
Green completed the victory with an easy tap-in into an empty net deep in stoppage-time.
Southend United: Bishop, Bwomono, Turner, Moore, Hart, Klass, Mantom (Kelman, 62), Dieng, Kightly (Bunn, 61), Cox, McLaughlin (Yearwood, 88). Unused substitutes: Smith, Kiernan, Lennon, Hyam.
Barnsley: Davies, Pinnock, Lindsay, Cavare, Pinillos, Dougall (Green, 76), McGeehan, Mowatt, Woodrow (Jackson, 89), Thiam (Bahre, 67), Brown. Unused substitutes: Walton, Williams, Hedges, Adeboyejo.
Referee: K Johnson (Somerset).