The 25-year-old produced a typically predatory finish in the fourth minute of time added on as Rovers beat their local neighbours to move them 11 points off the top six.
Blackburn boss Gary Bowyer was true to his pre-match promise to start Rhodes, who the east Lancashire club insist is not for sale despite Middlesbrough’s attempts to pry him away with a mooted loan move ahead of a permanent switch in the summer.
It appeared as if he had squandered the best chance of the night with a 79th-minute header which was brilliantly stopped on the line by Bolton goalkeeper Ben Amos.
However, as the game headed towards a goalless draw, he pounced to poke home after Doneil Henry had flicked on Tom Cairney’s corner.
Rhodes is no stranger to speculation but while he scored with his first chance against Bournemouth back in August when a bid from Hull was rejected that morning, he was otherwise largely anonymous for most of the game while fresh rumours of his future circulated.
For all the pre-match amble about Rovers’ striker, it was the front men at the other end of the pitch who looked to make the first real contribution.
Emile Heskey won a free-kick 20 yards out after a sliding challenge from Henry and Adam Le Fondre’s try was pushed behind by Jason Steele’s fists.
Le Fondre was lively but Steele was again alert to a sweetly-struck effort from range.
Cairney controlled proceedings from Rovers’ centre midfield and after firing just wide himself, his glorious defence-splitting pass was then almost capitalised on by Ben Marshall.
Blackburn were forced into two first-half changes through injury, with Corry Evans and Markus Olsson both being forced off, but they ended the opening 45 minutes in the ascendancy.
Craig Conway drilled narrowly past the post before picking out Marshall with an eight-yard header which he just could not keep down.
The hosts were slowly grasping the initiative in the second period and after Rhodes glanced an unconventional header wide while nearly down on his knees, Rovers bombarded Amos’ goal with a flurry of chances.
First, the on-loan Manchester United keeper thwarted Chris Brown at his feet following a smart one-two with Cairney and the ex-Hull midfielder then drew Amos into a fingertip save with a left-footed attempt from range.
From that resulting corner Henry brilliantly met Cairney’s corner but could only direct the header wide of the near post.
When Bowyer introduced top scorer Rudy Gestede from the bench with 20 minutes to go it was Brown, not the ineffectual Rhodes, who was withdrawn.
The game opened up in the final stages and both goalkeepers produced magnificent saves to preserve their clean sheets.
Steele stopped Neil Danns’ 30-yard piledriver and substitute Craig Davies’ one-on-one chance after Le Fondre’s flick-on had sent him clear.
At the other end, Amos’ brilliant denial of Rhodes stopped him from adding his 13th goal of the season from a Conway cross while Steele would match that with a near-post reaction save to repel Le Fondre.
But it was fittingly to be Rhodes’ night as he found himself all alone three yards to direct home the winner and perhaps strengthen Rovers’ position of not selling him to a division rival.