Albion had nothing to show for extended periods of possession in the first half and, after their goalkeeper Tomasz Kuszczak denied Jason Lowe and Morten Gamst Pedersen, Jordan Rhodes fired Rovers ahead from the penalty spot on the stroke of half-time.
A magnificent late Kuszczak save prevented the in-form Scotland international striker from adding to his tally and it would prove a vital intervention in the npower Championship tussle.
In the last of five additional minutes, Blackburn substitute David Goodwillie untidily sent Lopez tumbling in the box, leaving referee Robert Madley with little option but to award a spot-kick.
Lopez picked himself up to coolly convert and move Brighton to within four points of the play-off places in seventh.
Having lost Appleton's first game at the helm, Blackburn are five points further back in 14th.
The Rovers boss made two changes in midfield as Simon Vukcevic and Ruben Rochina made way for Pedersen and Markus Olsson.
Spanish playmaker Vicente was handed his first league start of the season by Poyet at the expense of Craig Mackail-Smith, while Gary Dicker replaced Dean Hammond in the Brighton midfield.
The visitors dominated possession during the opening stages and Ashley Barnes might have put them ahead in the 10th minute, failing to connect with Lopez's corner having found space.
But life on the counter-attack suited Rovers and Kuszczak was forced to keep Lowe's prodded effort out of the bottom corner following a driving run from Kazim-Richards.
An arching strike by Liam Bridcutt had Kuszczak's opposite number Jake Kean scrambling for the far post it dropped beyond midway through the half as the hosts struggled for a midfield foothold.
Yet Poyet's men created little of note and Blackburn appeared to grow into the contest around the half-hour, with Adam El-Abd blocking a Kazim-Richards shot from Martin Olsson's cross before Kuszczak fisted a swerving Pedersen long-range effort clear.
The pressure told as the half came to a close when El-Abd bundled Pedersen to the ground from Martin Olsson's left-wing delivery.
Madley remained unmoved but his assistant was well placed to flag for a penalty that Rhodes duly dispatched, sending Kuszczak the wrong way for his fifth goal in as many league matches.
Having watched his team resume proceedings on the back foot, Poyet decided to act nine minutes into the second half by sending on Will Buckley and Mackail-Smith in place of Vicente and Andrea Orlandi.
Goalmouth action had become virtually non-existent by the time Kazim-Richards turned to curl a low 25-yard drive past Kuszczak but into the side-netting.
Brighton's third substitute, Will Hoskins, gave Kean a first save of note in the 76th minute, but his near-post effort was weakly struck.
At the other end Kazim-Richards remained Blackburn's primary threat, bamboozling El-Abd with some clever footwork before Kuszczak pushed his shot over.
The former Manchester United goalkeeper saved his best work for the 84th minute when he somehow clawed Rhodes' looping header out of the far corner.
Lopez headed onto the roof of an unguarded net when Kean punched uncertainly at the start of injury time but he would soon be the hero.
- Sports & Recreation