The Lancashire side climbed out of the bottom three by virtue of a vastly improved second-half performance.
A win for Middlesbrough would have guaranteed top-flight status, but they now face a tense finale.
This was an extraordinary game in that the home side could have had the points wrapped up in the opening ten minutes but for the brilliance of goalkeeper Ali Al-Habsi.
Al-Habsi defied Boro as the home team produced their best attacking spell of the season.
Middlesbrough were without goalkeeper Mark Schwarzer, who was ruled out with a back injury, with Ross Turnbull making a rare first-team appearance.
But Bolton were without suspended Kevin Davies following his tenth booking of the season in the 1-0 home win over West Ham last weekend.
Middlesbrough began at a tremendous pace and central defender David Wheater nearly gave them the lead after two minutes.
Al-Habsi also produced a brilliant save from Sanli Tuncay, while Julio Arca shot over the bar.
Middlesbrough were the much more impressive first-half side and the first serious scoring attempt by Bolton came after 29 minutes when Turnbull saved from Matt Taylor.
Just before the break, Bolton suffered a blow when Tamir Cohen went off with a head injury and was replaced by Danny Guthrie.
Gary Cahill also suffered a head wound but he returned for the second half.
After the break, Bolton came out of the traps and looked more determined and suddenly Middlesbrough had lost their grip.
Grzegorz Rasiak headed against the crossbar from Taylor's right-wing corner.
Bolton were playing with much more spirit and Middlesbrough were fortunate to survive when Luke Young headed off the line from Guthrie, while Taylor hit a post.
However, the visitors went ahead after 59 minutes when Turnbull saved from Cahill, but Gavin McCann was right on the spot to score from a yard out.
Bolton manager Gary Megson was a jack-in-the-box in the technical area as he urged on his relegation-fighting side.
Middlesbrough struggled to find a way through a strong-tackling defence.
The defeat left Middlesbrough deflated but in a way it emphasised just how inconsistent Gareth Southgate's team have been this season.
In the previous home game, they had held the might of Manchester United to a 2-2 draw.