Middlesbrough skipper Emanuel Pogatetz was booked in the seventh minute for a foul. It proved an expensive challenge because Bolton went ahead with the resultant free-kick.
Matt Taylor crossed from the right to the far post where Gretar Steinsson connected with a header and the ball ended up in the back of the net as Kevin Davies challenged for it.
Before Boro had recovered Taylor had increased the lead from Steinsson's pass although Gareth Southgate would have been annoyed about the lack of a challenge on the scorer.
David Wheater headed wide for Middlesbrough as the home side piled on the pressure in a bid to get back into the match.
However, Bolton's well-drilled defence handled everything that was thrown at them and there was no chance of a breakthrough before the interval. Middlesbrough fans became frustrated and there was some booing at the half-time whistle.
Boro began the second half with an all-out assault against the packed defence. Bolton refused to panic though and goalkeeper Jussi Jaaskelainen was rarely called into action.
The visitors in fact had a great chance to increase the lead but Fabrice Muamba shot wide with an opening created by Johan Elmander.
Middlesbrough sent on substitute Adam Johnson at the expense of former Arsenal forward Jeremie Aliadiere and then withdrew ineffective Brazilian striker Afonso Alves and sent on Marvin Emnes in a bid to save the game.
Skipper Pogatetz lifted the crowd when he crashed the ball into the net following an overhead Wheater kick.
Bolton however crushed any hopes of a point-saving rally when Elmander almost immediately restored their lead.
It was the first goal by the record £10million signing since the opening game of the season against Stoke City.
Bolton manager Gary Megson would have been happy with the display of his team but it is back to the drawing board for Southgate.
The Boro boss, no doubt, will be hoping for a vastly improved display in the north-east derby against Newcastle United next Saturday.