Mason Mount's inch-perfect assist stunned domestic double-winners City at the Estadio do Dragao, as Chelsea claimed their second Champions League title to etch boss Thomas Tuchel's name into the Stamford Bridge annals.
Kevin De Bruyne suffered a facial injury on a wretched night for the stellar Belgium star, who will be an immediate injury doubt for the European Championships.
Pep Guardiola fielded a surprise pivotless midfield in a bid to catch out Tuchel and the Blues, but the move backfired and City paid the toughest price.
When Chelsea paid Bayer Leverkusen £70million for Havertz last summer eyebrows were raised in some quarters, but Chelsea were convinced of the 21-year-old's pure talent.
And now the classy forward has ended a testing campaign that included a battle with Covid-19 with a goal of the utmost quality - on the highest stage and at the perfect time.
In just 124 days Tuchel has transformed Frank Lampard's muddled men into mean tactical machines - and champions of Europe.
Guardiola has spent five years honing City for European dominance, but that frustrating wait goes on.
The former Barcelona and Bayern Munich boss last won the Champions League in 2011, the year before Chelsea's first European triumph.
Chelsea's third win over City in six weeks clearly ranks most highly, but also cements Tuchel's arrival as a genuine tactical master.
The spectacular transformation has owed as much to sharp tactical acumen as shrewd people management.
Any fears of a tight affair were immediately dispelled at the top of the night.
Timo Werner missed his first of two sitters when Havertz cut back to him in the area, while Ben Chilwell had to conjure a full-stretch clearance at the other end.
Werner's second miss was almost a bigger let-off for City than the first, as the Germany striker overran Havertz's inside ball, muddled up his feet and scuffed a low-power effort for an easy Ederson save.
Just when the half looked to peter out goalless though, Mount spun on the ball on the left wing and delivered the killer long-range through-ball for Havertz.
Werner raced out to the left to create the space, Havertz ghosted through and nicked the ball around the fast-advancing Ederson - before tapping into the empty net.
Chelsea had lost influential centre-back Thiago Silva to a groin injury just past the half-hour, but Guardiola resisted the temptation to make his own half-time changes, and while City pushed higher upfield N'Golo Kante produced a stunning cover tackle on De Bruyne.
The Belgium star's night went from bad to much, much worse moments later, when colliding with Rudiger. After lengthy treatment the ex-Chelsea playmaker trudged off in tears, with a possible broken cheekbone.
Guardiola eventually gave up the ghost on his pivot-free midfield just past the hour, with Fernandinho replacing Bernardo Silva and moving the ball in their neat patterns.
Seven minutes of added time left Chelsea players and fans biting nails, and Mahrez so nearly equalised with a snap shot at the very, very last.
But the ball sailed just wide, and Chelsea were champions of Europe again.