In a tightly fought contest on Teesside, Boro went ahead in the 81st minute through a Grant Leadbitter penalty.
Two minutes from time, Jermaine Beckford had the opportunity to rescue a point for the Whites, again from the penalty spot, after Andre Moritz was fouled, however the striker was unable to keep the ball on target and skied his kick over the bar.
Manager Dougie Freedman named an unchanged side from the one that beat Watford seven days ago at Vicarage Road.
Striker Joe Mason, who joined the Whites on loan from Cardiff City on Wednesday, was named amongst the Bolton substitutes for the clash on Teesside.
Hosts Middlesbrough, who welcomed new head coach Aitor Karanka to the Riverside for the first time, handed Shay Given his first start for the club following his temporary switch from Aston Villa 48 hours previous.
It was an electric atmosphere ahead of kick-off, with the Boro faithful giving their new boss a warm welcome but the Riverside crowd soon quietened down with neither team able to influence the game inside the opening 20 minutes.
It was a frustrating start to proceedings for both respective managers, with the first talking point coming in the 23rd minute when Leadbitter was handed a yellow card for a strong challenge on Bolton skipper Jay Spearing.
The real battle of the first half took place in the midfield area as both the Whites and Boro battled for possession.
With ten minutes to go before the half time interval, the tempo gradually started to rise as Wanderers won three successive corners but were unable to test former Newcastle United custodian Given.
The best opportunity of the half fell to the hosts in the 39th minute. Winning their first corner of the game, Leadbitter delivered a deep cross into the penalty area for the delayed run of Ben Gibson but the Boro academy graduate powered a header narrowly over the bar.
Both teams were unchanged for the start of the second half but there was certainly a difference in how the game was being played with a faster rhythm compared to the first 45 minutes.
The fans were seeing a far more entertaining contest and within eight minutes of the restart, Bolton put together a lovely quick passing move involving Chung-Yong Lee and Spearing, resulting in striker Jermaine Beckford having full sight on goal but his close range effort was wayward and caused no concern for Given.
Four minutes later and Jamaican international Beckford went close again as Wanderers went in search of their fourth successive win on the road.
A long ball upfield from Kevin McNaughton inside the Boro penalty area dropped over the head of Beckford who tried a first time volley, only to rise over the bar.
As the clock ticked past the hour mark, referee Mark Brown waved away strong appeals for a penalty from Bolton as Beckford looked to have been pushed in the back by a Reds defender.
At the opposite end of the field, Middlesbrough substitute Curtis Main came dangerously close to breaking the deadlock as he let fly a left footed strike from 20 yards which crept inches wide of the post.
Wanderers boss Freedman made his first change of the afternoon with 25 minutes remaining as Pratley makes way for Andre Moritz for the second consecutive game.
With nine minutes to go, the hosts were awarded a spot kick as centre back Tim Ream was alleged to have dragged Middlesbrough’s second substitute of the afternoon Marvin Emnes to his feet just inside the penalty area.
Goalkeeper Andy Lonergan was faced with the task of denying Grant Leadbitter his fourth goal of the season but the former Sunderland man sent the Wanderers custodian the wrong way to hand his side the lead.
Boss Freedman responded to Middlesbrough’s opener by bringing on French striker David Ngog and fellow attacker Joe Mason, with the latter making his debut for the club.
Despite Middlesbrough taking the lead, Wanderers didn’t let their heads drop and went in search of an equaliser on the Riverside to maintain their unbeaten league run which stretches back to September.
And two minutes remaining, Bolton were given a glorious chance to tie matters when Moritz was hacked down just inside the box, with referee Brown having no alternative but to point to the spot.
Top goal scorer Beckford stepped up but unfortunately the striker couldn’t keep his effort on target and the ball sailed harmlessly over the bar as Boro held on for all three points.
Wanderers will now be looking for an immediate reaction as they welcome Huddersfield Town to the Reebok Stadium on Tuesday evening, 8pm kick off.