David Wheater's first Premier League goals for three and a half years were the difference in the first half, both headers from close range.
However Rovers will be upset that Junior Hoilett was denied a penalty at 0-0 after Gretar Steinsson took him out inside the box.
Steven N'Zonzi flicked home from a Morten Gamst Pedersen long throw in the second half for Blackburn, but they were unable to find an equaliser.
Bolton, playing their first game since Muamba suffered a cardiac arrest on the pitch in the FA Cup tie at Spurs, were unchanged from their last Premier League match against QPR. Muamba came on late in that match.
There were touching tributes at the Reebok, with fans holding up cards to form a 'MUAMBA 6' mosaic and the home substitutes bearing the player's number on their bibs.
Blackburn went with the same XI that beat Sunderland on Tuesday evening.
Bolton saw more of the ball in the early stages with Martin Petrov's left foot causing problems for Rovers. Aside from crosses, he tested Paul Robinson with a swerving drive from distance on nine minutes.
Adam Bogdan dropped the first of several catches soon afterwards on a nervy afternoon for the home keeper.
On 23 minutes, on a rare attack for Blackburn, Hoilett drove through three Bolton defenders and into the box. Despite Steinsson clearly impeding him as he stepped across him, referee Andre Marriner refused to award a spot-kick.
Yakubu was just late in sliding to meet a Marcus Olsson cross from the left as Blackburn came increasingly into the match - but were dealt a blow two minutes further on when Bolton took the lead in the 29th minute.
Petrov delivered from the left and his cross skimmed off a Blackburn head on its way to Wheater, who nodded into the corner.
Darren Pratley headed a similar chance over then, at the other end, Yakubu stooped to head an excellent Marcus Olsson cross wide of the near post when unmarked.
Steve Kean's side lived to regret that wasted chance as Ryo Miyaichi found the head of Wheater with a corner on 35 minutes, and the centre-half made no mistake to beat Robinson a second time.
Six minutes into the second period N'Zonzi almost beat Bogdan with a flick from a long throw, similar to the chance he would later score from, while David N'Gog should have scored for Bolton with a free header provided by Petrov.
Wheater wanted a penalty when Scott Dann seemed to drag him down before N'Zonzi pulled one back for Rovers in the 56th minute with Bogdan redundant on his line.
Immediately Mark Davies then missed a sitter with his head from a Miyaichi cross and, with the game suddenly flowing from end to end, Hoilett was embarrassed to completely miss the ball while attempting to control a Martin Olsson cut-back and Pratley also should have nailed a header from six yards without a Rovers defender in sight.
With the clock ticking down, Bolton retreated to their penalty area and consequently invited pressure upon themselves and keeper Bogdan. Hoilett caused trouble with mazy dribbles and low crosses, but it was the long throws and free-kicks that had Bolton fans sweating.
Robinson came up for a last chance and arrived free at the back post to dive comically for a header, but the ball was beyond him.
And Bolton held on to claim back-to-back league wins for the first time in 11 months and move within two points of Blackburn with a game in hand.