Havertz and Mason Mount combined to score the only goal as Chelsea secured their second Champions League name and prevented Man City from lifting the trophy for the very first time.
Thomas Tuchel, who replaced Frank Lampard from the Stamford Bridge hot-seat in January, dropped last season's Champions League final with PSG but it was a different outcome for the German boss now around, since his team denied Premier League champions City a sensational treble.
Pep Guardiola had lost one of his 14 major finals as a manager before tonight, but the Manchester City manager was left disappointed as he failed to win his third Champions League and first because 2011.
On a balmy evening in the Estadio do Dragao stadium, Guardiola opted to exit both Fernandinho and Rodri and said he desired his City staff to'assault' Chelsea.
Both teams created early openings, with Edouard Mendy and Reece James needing to unite to stop Raheem Sterling a goalscoring chance after the England forwards was playing by goalkeeper Ederson.
Timo Werner then wasted his first prospect of the game, scuffing a cross from Ben Chilwell to the frustration of the 6,000 Chelsea fans in attendance.
Werner saw a tame effort easily saved by Ederson just minutes later, but just following Chilwell made a crucial interception as Riyad Mahrez appeared to be pulling the cause for the opening goal.
Chelsea's defence was lauded since Tuchel's appointment at the start of the year and Antonio Rudiger followed Chilwell's case when he denied Phil Foden with a dazzling last-ditch tackle.
But when Chelsea were bemoaning their fortune since Silva hobbled off, their disposition soon improved as Havertz opened the scoring with his first Champions League goal for the Blues.
Mount, that has enjoyed yet another breakthrough year at Stamford Bridge, located Havertz with a brilliant through ball and the Germany international rounded Ederson well before slotting into an empty net.
Perhaps unsurprisingly, given the hectic nature of the opening 45 minutes, the second half began in more subdued style.
Neither side was able to make any primitive opportunities and Manchester City's mood dampened farther when Kevin de Bruyne was forced off with a nasty eye injury following a collision with Rudiger.
City finally produced a telling move on 68 minutes; Mahrez's crossover seemed destined to be tapped in by Ilkay Gundogan however Chelsea captain Cesar Azpilicueta was on hand to intercept.
Chelsea were largely happy for City to control possession but they had a huge opportunity to score themselves and put the match to bed with 20 minutes remaining.
Tuchel's side broke with purpose and speed but following a good move, second-half substitute Christian Pulisic's chipped effort flew wide of the article.
Man City looked for inspiration from club legend Sergio Aguero, making his final game for the club, although not even the Argentine legend could discover a way through Chelsea.
Mahrez came sending the match to extra-time -- his late attack from the edge of the box flew just over the bar -- but Chelsea were soon celebrating their next Champions League triumph.
Soon after the last whistle, Chelsea goalscorer Havertz stated:'I don't know what to say. I truly don't know what to say. I waited a long time.
'Now I would like to thank my family, my parents, my grandmother and my girlfriend. I don't know what to say. I've waited 15 years for this moment and now it's here'
