Meanwhile, the Trotters all but secured their safety as goals from captain Kevin Davies, Gary Cahill, Matty Taylor and Ricardo Gardner moved Wanderers to 37 points with seven games still to play.
Boro, who had equalised through a neat Gary O'Neil finish late in the first half, are five points adrift of safety in the bottom three after a record ninth straight away defeat.
The hosts set off like a tracer bullet as Davies scored his 12th goal of the season to ease the pain of being rejected by England boss Fabio Capello earlier this week.
Davies clipped home a deep left-wing Gardner cross in the eighth minute and Bolton looked dangerous every time they went forward in the opening stages.
But Gareth Southgate's men came back into things as the half progressed, with Afonso Alves hitting the post with a free-kick and Tuncay Sanli having a goal ruled out for offside.
Moments later, in the 38th minute, O'Neil latched onto Tuncay's throughball to neatly clip over the advancing Jussi Jaaskelainen.
But all Boro's hard work was undone soon after when they let in the home side for their second of the afternoon.
Tuncay fouled Gretar Steinsson on the right, leaving Taylor to fire a free-kick into the box.
Boro failed to clear despite the opportunity to and Johan Elmander found Cahill in space to give Bolton the lead again two minutes before the break.
That seemed to knock the stuffing out of Boro, who knew it was not going to be their day when the impressive Taylor - a former transfer target before he headed to the north west last January - curled a fortuitous free-kick in with 22 minutes left.
Taylor whipped in his delivery from 35 yards out only to see Boro's defence leave it and let it notch into the top left corner.
And when Taylor delivered again, this time from the left, Jamaican speedster Gardner controlled it at the back post before curling past Brad Jones.