The 35-year-old academy manager was promoted to fill in after Andy Ritchie was controversially sacked and he is in charge at least until after the Elland Road clash with Leeds on Saturday.
After Saturday's injury time win over Ipswich, the Yorkshire side produced another welcome win over rock-bottom Southend to drag themselves out of the bottom three courtesy of goals from Brian Howard and Kyel Reid.
Barnsley came close to an early goal in the first minute but Darryl Flahavan held on to a stinging shot from Neil Austin from outside the area.
At the other end winger Jamal Campbell-Ryce did well cutting inside before threading a neat ball for Lewis Hunt but Nick Colgan made a comfortable save.
But Barnsley were denied by the post a minute later after a corner from oward fell for Antony Kay and his drive was flicked on to Marc Richards but he hit the upright from close range.
Leon Knight, in his second start since arriving from Swansea last week, gave Southend problems and forced Efe Sodje into a rash challenge that earned him booking.
And Knight was involved when Barnsley took the lead after 24 minutes with a well-worked goal.
Knight slipped in Richards who made ground into the area and fired a low ball across the face of goal to find Howard who crashed a shot home from five yards.
Barnsley continued to play neat an open football with Howard impressing and they might have stretched their advantage seconds before half-time when Knight twisted and turned on the edge of the box but saw his low shot well held by Flahavan.
Sam Togwell stretched to try and add to Barnsley's lead early in the second half but Sodje did enough to unsettle the midfielder as he poked at a shot.
Frustrated Southend star Freddy Eastwood was booked when he lashed out at Togwell.
Substitute Reid - on loan from West Ham - added a second for Barnsley three minutes from the end but then was sent off for a second bookable offence.