Los Blancos had to ride their luck in the first period, with BVB comfortably the better side, but the Bundesliga outfit were ultimately made to pay for their missed opportunities.
Dani Carvajal sent Carlo Ancelotti's side ahead in the 74th minute, before Vinicius Junior doubled their advantage in the 83rd minute, and Dortmund were unable to respond, with Real Madrid once again cementing their spot as the best side in European football.
It is a La Liga, Supercopa de Espana and Champions League treble for Los Blancos this term, but Dortmund deserve huge credit for their progression to the final, and the German outfit can take plenty of heart from what was a strong performance for long stages of the showpiece event in the English capital.
Carvajal, Vinicius score the goals for Real Madrid
With Aurelien Tchouameni out of the final through injury, Eduardo Camavinga came into the Real Madrid midfield, and the Spanish giants were otherwise as expected, with Nacho given the nod in the middle of the defence alongside Antonio Rudiger, while Thibaut Courtois started in goal.
Dortmund had Jadon Sancho, Julian Brandt and Karim Adeyemi in support of centre-forward Niclas Fullkrug, with Marco Reus on the bench in his final game for the club.
Federico Valverde fired over the BVB crossbar in the 12th minute, but it was Dortmund that dominated in the period that followed, with the Bundesliga giants causing all sorts of problems with their pace.
Brandt placed one just past the post in the 14th minute, before Adeyemi managed to round Courtois seven minutes later, but he took it just too wide, and Carvajal was across to make the challenge.
Fullkrug was next to come close, hitting one off the base of the post, before Courtois was forced into a smart save to deny Adeyemi, with the attacker's running power causing so many issues.
Dortmund were made to pay for missed chances
Nico Schlotterbeck also tested Courtois late in the first period, and Dortmund really should have been ahead at the interval, but Real Madrid managed to enter the break on terms.
The Spanish outfit's two shots in the first half proved to be their joint-fewest in a first half of a match across all competitions during the 2023-24 campaign, but there was an instant improvement at the start of the second period, with Toni Kroos, on his final showing for Los Blancos, forcing Gregor Kobel into a smart save from a bending free kick.
Carvajal then headed over from the resulting corner, before the right-back had a strike deflected into the body of Kobel by Maatsen, with Real Madrid looking more dangerous in the second period.
Courtois was again called into action in the 63rd minute to keep out a header from Fullkrug; Vinicius then nodded wide down the other end, with the score still level heading towards the 70th minute.
Real Madrid continue their European dominance
Jude Bellingham was inches away from making contact on a dangerous Vinicius delivery in the period that followed, with the ball dropping just wide of the Dortmund goal.
Real Madrid did make the breakthrough in the 74th minute, though, and it came from an unlikely source, as Carvajal headed a corner from Kroos into the back of the net.
Schlotterbeck made a wonderful challenge to prevent Bellingham from potentially sending Los Blancos 2-0 ahead in the 77th minute, with the Englishman's effort being deflected just wide of the far post.
Real Madrid were dominant, with Kobel doing brilliantly to keep out Camavinga and Nacho in quick succession, but the Spanish giants had their second in the 83rd minute through Vinicius, with the Brazilian sweeping one into the corner after being found by Bellingham.
Fullkrug thought that he had set up a grandstand finish at Wembley when he found the back of the Real Madrid net late on, but his effort was quickly disallowed for offside, and Real Madrid closed out the final stages to make it 15 European Cups with a two-goal success at Wembley.