Eagles, also a star performer when Wanderers dispatched Rovers 2-1 at Ewood Park in November, was granted a hostile reception from the visiting support upon his 71st-minute introduction in place of Darren Pratley.
But the 27-year-old had the last laugh as he drove at the Blackburn defence in the third and final minute of stoppage time to send home a low 25-yard drive via the inside of the post.
Late drama appeared on the cards as a turgid contest sprung to life in the final ten minutes - Blackburn's top scorer Jordan Rhodes was twice denied by Andy Lonergan in the Bolton goal, while Lee Chung-Yong saw an effort cleared off the line by Adam Henley.
Lonergan made his league debut in goal for Bolton as Adam Bogdan failed to recover from a groin injury, while January signing Medo Kamara was handed a maiden Wanderers start in midfield.
Appleton made four changes to the side the that lost 3-2 to Peterborough on Saturday, with full debuts for loanees Cameron Stewart and David Jones as fellow midfielder and club captain Danny Murphy was omitted from the matchday squad.
Marcus Olsson saw a speculative effort deflected behind by Zat Knight but, as has been the case far too often this season, Blackburn offered little in the way of a sustained attacking threat during the opening 45 minutes.
The hosts fared little better and, after Jay Spearing offered Kean a routine stop from distance, Rovers almost took the lead when Grant Hanley side-footed Morten Gamst Pedersen's 41st-minute free-kick over the bar.
Blackburn began the second period with greater intent and Lonergan excelled himself in touching Hanley's looping header behind following a period of set-piece pressure.
Leon Best came on for DJ Campbell in the 80th to make a Blackburn debut cruelly delayed by pre-season cruciate ligament damage and the Republic of Ireland international instantly created his side's best chance, playing in Rhodes to be thwarted by Lonergan.
At the other end, Eagles saw a deflected effort loop wide with Kean scrambling. The Blackburn goalkeeper was far more assured in the 85th minute, saving well from Kamara's rasping drive before Henley cleared Lee's follow-up from the goalmouth.
Rhodes headed goalwards to bring another stop out of Lonergan and Jones lobbed onto the roof of the net as Rovers threatened to finish the stronger, but Eagles had other ideas and sprinted the length of the field in celebration underline his point to the visiting fans.