Goals from Kevin Davies and Bruno N'Gotty gave Bolton a lift up the table at a sun-soaked Reebok Stadium.
However, Boro manager Steve McClaren has now got deep problems after picking up only one point from five matches.
Bolton manager Sam Allardyce stuck by the same Wanderers team that ended the game in the 0-0 home draw against Charlton.
New signing striker Mario Jardel made the substitute's bench.
McClaren brought in winger Boudewijn Zenden for his debut and Wanderers old boy Michael Ricketts was named substitute.
Bolton broke almost from the kick-off and Boro keeper Mark Schwarzer had to race out of his area to block an attempt from Davies.
Middlesbrough quickly settled and held the ball for long periods and a shot on target by new signing Zenden was parried away by Jussi Jaaskelainen.
The visitors kept the pressure on and the home defence was at times stretched and Jaaskelainen had to pull off a fine save from a 20-yard power drive by Jonathan Greening.
After 23 minutes Bolton broke out of defence and won a corner on the right. The resulting inswinger from Stelios Giannakopoulos was headed in at the far post by summer signing Davies.
Bolton's joy was tempered when defensive stalwart Florent Laville had to be stretchered off after twisting his knee - N'Gotty filling his place.
Szilard Nemeth should have equalised for the Teessiders on a one-on-one with Jaaskelainen but his shot flew wide off the keeper.
Ricketts came on for Nemeth at the start of the second half and was soon involved in the action but after beating a defender and running in along the goal-line, his cross was not met by anyone.
After that it was all Bolton with Youri Djorkaeff and Jay Jay Okocha causing the Boro defence to panic.
Bolton doubled their lead after being awarded a free kick on the left. A fine curling cross from Giannakopoulos was headed home by N'Gotty who unfortunately picked up a yellow card for over-celebrating his goal.
On the stroke of full time, Jaaskelainen was able to save Ricketts' headers easily.