Despite residing in the bottom half as recently as matchday 27, five wins from their previous six have catapulted Dortmund into top-four contention, but securing a crucial win over last season’s champions was never going to be easy.
Leverkusen, driven forwards by the menacing Florian Wirtz, dominated the opening exchanges and forced Gregor Kobel into a string of saves, and they remained on top until notching the opener just after the half-hour mark.
Wirtz exchanged passes with Jeremie Frimpong, allowing the latter to whip a left-footed shot into the far top corner.
The entire Leverkusen XI rushed to embrace Alonso, who will leave the club at the season’s conclusion, but the celebrations were short-lived.
Just over a minute later, Pascal Gross played Karim Adeyemi to the right byline, and the Germany international striker played a clever ball in for Julian Brandt to sweep home.
That was Dortmund’s first opportunity, and they punished the hosts’ wastefulness again with their next.
Brandt’s ball was helped on by Gross to Julian Ryerson, who gave Lukas Hradecky no chance with a powerful low drive into the far corner.
More saves from Kobel - and a strike against the bar from Amine Adli - kept Dortmund in front at half-time, and they could easily have doubled their advantage when Adeyemi almost connected with Daniel Svensson’s ball across the face.
Alonso introduced Patrik Schick in an attempt to respond, but his side subsequently capitulated as Leverkusen suffered their joint-worst home league defeat since the Spaniard took charge.
Adeyemi struck across Hradecky and into the top corner, having been released by a penetrating Brandt ball, before Serhou Guirassy took advantage of a mistake to bury it inside the near post, with that strike making him the joint top-scorer in the league of any player in a debut season at BVB.
It just hadn’t been Leverkusen’s day, but they did get a consolation when substitute Jonas Hofmann acrobatically headed in Wirtz’s trivela cross.
The win puts Dortmund just a point behind fourth-placed Freiburg, but even in spite of their far superior goal difference, Niko Kovac will know that a win is likely required against relegated Holstein Kiel next weekend.
Meanwhile, most of the talking points at Leverkusen surround next season, with Como boss Cesc Fabregas hotly tipped to take the reins at the BayArena when Alonso departs at the end of this campaign.
Flashscore Man of the Match: Julian Brandt (Dortmund)