Bolton's on-loan midfielder Neil Danns bagged the only goal of the game with a perfectly-placed curling effort in the 64th minute to ensure an unhappy Oakwell return for Wilson following 15 years away.
Bobby Hassell, Jim O'Brien and Peter Ramage all went close for the home team in the opening 45 minutes but they offered little after the break.
The result means the Tykes remain bottom of the Sky Bet Championship, four points from safety, while Bolton move eight points clear of the relegation zone.
Wilson, who left the Tykes for local rivals Sheffield Wednesday in 1998 before returning on December 17, saw his team fail to score for the second successive game and said goalscoring was a problem.
"The three or four good chances we had, we just can't seem to get our noses in front at the moment," Wilson said. "I think if we do that, you see a different team.
"If you don't score, you're always playing on the edge and we were undone by a bit of quality from their perspective.
"When you see the quality in their side, to keep it at bay for long periods is a job in itself but they did open is up for a period of 10 to 15 minutes in the second half in particular.
"We managed to steady ourselves and got good shape again and negated a little bit of their attacking play but, again, we couldn't seem to force it in the net at the other end and that's obviously a problem they've (the Barnsley players) had all season.
"You've got to look at who you're playing against as well; they're a quality side. They know how to see a game out and how to nullify when they've got their noses in front - that's the sign of a good side. I don't think it's a sign of us not being able to get back in the game, I don't think they allowed us to do at times."
Bolton boss Dougie Freedman was pleased to take all three points from a hard-fought game.
He said: "I think it was a very difficult match for us. I felt, first half, it was a very tight game, not a lot in it. I think we showed defensive quality.
"Second half, the game opened up. Barnsley were looking to win the game, we had to defend very resolutely in the second half, especially in our box.
"But, because the game opened up, it gave our attacking players more space to play in, we created more chances, we had more pressure on their goal and I think, in the end, we deserved to win the game.
"When I go home tonight and analyse it, it was pretty much a good, solid performance from us from a very difficult game.
"This is the third - it must be a record - new manager we've faced away from home in a row (following trips to Middlesbrough and Wigan) so it's difficult for us.
They were up for it, the crowd were up for it, so it's very pleasing to get the win today, especially in the circumstances."