The 30-year-old, who averages one a season, produced a sparkling opener to put his side on the route to a cash bonanza if Spurs overcome Cardiff.
Striker Lee Bradbury sealed the victory by snapping up his third of the season with a helping hand from a mistake by Paul Reid.
Barnsley, still without a win since caretaker-boss Simon Davey was given the job on a permanent basis, might have gone ahead after 20 minutes.
Paul Hayes darted down the left and had the visitors in trouble with an accurate cross but Darryl Flahavan produced a super reaction save to turn away a goalbound header from Danny Nardiello.
And when a poor clearance from Flahavan gifted Barnsley a chance, Martin Devaney's tame shot was easily collected by the keeper.
But seconds later the visitors went in front with Maher's super finish. He collected the ball outside the area and as Barnsley backed off to watch he curled a splendid shot out of Nick Colgan's reach.
A minute later Barnsley should have been level when Brian Howard shot from 15 yards with Flahavan sprawling on the ground but the shot cannoned out of defender Adam Barrett.
Hayes might have levelled for Barnsley when he cut in from the left but Flahavan did well to hang onto his searing low shot.
Southend came close to stretching their lead but leading scorer Freddy Eastwood curled a 20-yard effort over and Jamal Campbell-Ryce was wide with a stinging angled effort.
Barnsley keeper Colgan fumbled another shot from Campbell-Ryce but recovered as Eastwood charged in to try and finish off.
Eastwood was within a whisker of adding to his 11-goal tally and killing off Barnsley five minutes into the second half when Mark Gower chipped a smart ball from the left but Paul Heckingbottom did enough to glance it over the striker as he sized up for a simple finish.
Barnsley would have levelled soon afterwards but for impressive stops from Flahavan.
Youngster Michael Coulson, who scored the controversial equaliser in the first match, should have scored but his low shot was cut out by the keeper who then pulled off two more saves from Hayes and Sam Togwell.
But Bradbury put the game beyond Barnsley with his third goal of the season after 58 minutes. A Blunder by Reid let in Eastwood who crossed for Bradbury and he controlled, spun and fired in from close range.