The 20-year-old midfielder, who is on loan from Manchester United, starred in the centre of the park for the Tykes but was unable to get his side over the line at Oakwell.
Ryan Colclough opened the scoring for the Railwaymen in the 14th minute before Alfie Mawson swiftly responded for the home side before Lauri Dalla Valle netted a winner for the visitors with just over 10 minutes remaining, deflecting a cross from Swansea City loanee Adam King past Barnsley keeper Nick Townsend with his chest.
The win was Crewe's second of the season but did not allow them to move off the bottom of the League One table as Barnsley dropped to 13th with a second-straight loss.
After the defeat, Pearson was named the Tykes supporters' player of the match as his second temporary spell in South Yorkshire continues to be a success.
Pearson's United colleague Joe Rothwell was an unused sub while Swans winger King went the full 90 for Crewe.
Man of the Match Ben Pearson presents today's match ball sponsor NG Decor with a signed match ball! #barnsleyfcpic.twitter.com/aQZTxPlyyy
— BFC Commercial (@BFC_Commercial) October 10, 2015