Stuart Gray and Guy Whittingham were placed in temporary charge this week and masterminded Portsmouth's third win of the season.
Barnsley had been the better side for much of the first half and struck the post through Jacob Butterfield.
But the home side were well on top when David Norris struck in the 61st minute and they quickly added a second through Luke Varney as Barnsley's seven-game unbeaten run came to an abrupt halt.
Barnsley created the first real opening in the eighth minute when Butterfield made space to fire in a well-struck shot which Portsmouth goalkeeper Stephen Henderson was able to push away.
Tykes defender Bobby Hassell then produced a mazy run from the halfway line and was able to surge into the penalty area before being thwarted by a last-ditch block from Ricardo Rocha.
Barnsley remained the more dangerous side and Ricardo Vaz Te wasted two great opportunities in quick succession midway through the first half.
Firstly he failed to pick out Butterfield when Barnsley poured forward on the counter-attack, and then he blazed over with the goal at his mercy.
Portsmouth created little until the 35th minute when Greg Halford rose highest to meet Liam Lawrence's corner but was unable to hit the target.
Just a minute later they threatened again when a neat passing move set up Norris and his attempted chip over Luke Steele with the outside of his right foot brought a diving save from the Barnsley goalkeeper.
The visitors went straight up the other end and went agonisingly close to breaking the deadlock as Butterfield's low shot struck the inside of the post and flashed across goal but stayed out.
Norris was then only narrowly wide with a long-range effort for Pompey as the half finished goalless.
Barnsley made a double change at the break, sending on Scott Wiseman and Cameron Park for Hassell and Vaz Te, but it was the home side that started the second half well.
Erik Huseklepp looked to have converted Lawrence's cross but Jimmy McNulty cleared off the line, before the breakthrough came in the 61st minute.
The ball dropped to Norris on the edge of the area and he took one touch to control the ball in the air before volleying an unstoppable low shot past Steele.
Just a minute later the lead was doubled when substitute Dave Kitson crossed from the right byline and Varney made no mistake from close range.
Henderson had to react quickly to tip over a Butterfield shot which took a wicked deflection and almost dropped under the crossbar as Barnsley tried to hit straight back but they never threatened a comeback.