It was the away side who had the first chance of the match in the opening minute when last week's goal hero Henrik Pedersen hooked the ball wide for Bolton in an attempt which Boro keeper Mark Schwarzer watched sail past his post.
Dutchman Boudwijn Zenden, the winning goalscorer for Boro in the Carling Cup then saw his free kick tipped away by Jussi Jaaskelainen in the Bolton goal in the sixth minute and ninety seconds later the home side took the lead when Bolton top goalscorer Kevin Nolan steered the ball past his own goalkeeper Jaaskelainen following a corner from Zenden.
Soonafter Pedersen was then to hit a post for Bolton in an attempt to bring them back into the game whilst at the other end Brazilian midfielder Juninho broke well on the counter attack but could not keep his shot down despite having Joseph Desire Job as an option as the Cameroonian was in acres of space.
Shortly before the half time break Juninho was once again foiled by Jaaskelainen having been set up well by Gaizka Mendieta. The Finnish keeper produced a superb reflex save to stop the midfielder from doubling Boro's slender lead.
Boro had been the better side in the first period as Bolton seemed a shadow of the team which had battled so gallantly in the win over Newcastle United just six days previously and it was no surprise that in the early stages of the second half the home side increased their advantage.
A deflected shot by Mendieta is converted by fellow midfielder Jonathan Greening on 51 minutes to make the scoreline 2-0. Just moments before Bolton captain Jay-Jay Okocha combined well with striker Henrik Pedersen but the Nigerian watched his shot sail agonisingly wide of Mark Schwarzer's goal.
With 20 minutes remaining substitute Javi Moreno had a chance to bring Wanderers back into the game but the Spaniard could not make the most of his chance after being put in a good position following a cross by Henrik Pedersen.
Okocha then had his free kick finely saved by Australian international Schwarzer whilst former Bolton striker Michael Ricketts was foiled at the other end in the closing stages of the game.
For Boro it puts some distance between themselves and the sides below them but for Bolton it will mean another week to wait until they can reach their target of 40-points.