The Trotters led 3-1 from last week’s first leg, but the Tykes pegged them back to within a goal when Sam Cosgrove opened the scoring nine minutes before half-time.
Bolton hit back though when Aaron Collins struck from distance, while Eoin Toal headed in from a corner to ensure the score was 5-2 on aggregate at half-time in the second leg.
Adam Phillips offered the Tykes a ray of hope with 64 minutes on the clock, when he received the ball from Cosgrove and applied the finish.
Cosgrove turned from creator to goalscorer when he grabbed his brace 12 minutes later, heading in Conor Grant’s ball from deep to bring Barnsley to within a goal of the Trotters.
The visitors then had a huge chance to level the tie, but Corey O’Keeffe’s delivery across goal was just missed by Cosgrove, while Mael de Gevigney failed to make the right connection at the back post.
Oxford United head to Peterborough United tomorrow night, looking to finish the job in their semi-final, after securing a 1-0 lead in the first leg, courtesy of Elliott Moore’s second half header.