After taking an early lead through Raul, Real had quickly conceded an equaliser to Bayer, through Brazilian Lucio.
But with seconds left in the opening half, a previously anonymous Zidane found a sublime volley that flew unerringly into the top right corner of Hans-Jorg Butt's goal, and sent the European Cup back to Spain.
It is impossible not to feel sorry for Bayer, so often the bridesmaids domestically, who threatened Real's control by laying siege to the Spaniards` goal in the latter stages.
Conceding on the stroke of half time cut the German side to the bone, and although they battled to get back into things, the newfound confidence of the Madrid side, and the sheer quality of their players gave them very little inroads until a thrilling final ten minutes.
After his goal Zidane was at the heart of everything, and his composure on the ball was a joy to watch, as the under-rated Santiago Solari and tough tackling Ivan Helguera bustled around.
It seemed like a long time since Bayer had dominated in the opening period, even after receiving the early shock of a Raul goal.
Klaus Toppmoller must have spent much of his week ensuring his players would not fall for the fancy footwork and lightning passing of the brilliant Real forwards, but he cannot have anticipated the horrors of conceding to a long throw and a bobbling shot.
Minutes after a similar occurrence, Lucio failed to track Raul, and Roberto Carlos hurled a long throw-in for the Spaniard to run on to.
Raul needed no second invitation and he scuffed an early shot that goalkeeper Hans-Jorg Butt inexplicably let trickle past his left hand and into the back of the net.
But the goal galvanised the Germans and not Real, and just six minutes later Michael Ballack was felled and Bernd Schneider handed the opportunity to curl a ball into the Real box.
The German international found the perfect delivery and Lucio atoned for his earlier momentary loss of concentration with a text book header from the edge of the six-yard box after losing his marker Fernando Hierro.
Bayer continued to take the lion's share of the possession but created little - although Thomas Bdaric wasted a glorious opportunity from a delightful flighted ball over the top from Ballack - delaying until the goalkeeper easily blocked his effort.
But with the game looking likely to end up level at half time, three world class players combined down the left flank to provide the truly memorable goal from Zidane.
Solari provided a delightful ball for Roberto Carlos to run onto and the speedy Brazilian hooked the ball back to the edge of the area.
There Zidane sized up the dropping ball before unleashing a perfect hooked volley into the top corner with his weaker right foot - a goal worth every penny of the world record £46 million Real spent to sign him from Juventus.
As the second half wore on Morientes saw Butt make a wonderful stop to what seemed like a sure goal, minutes after substitute Dimi Berbatov headed woefully over the bar when well placed.
Real finally began to realise that they were only 15 minutes from lifting the cup - and they duly froze, allowing the Germans to throw everything forward.
Goalkeeper Cesar had been forced off with an injury, and it was reserve Iker Casillas that stood in the German side's way - as seven minutes of injury time was displayed.
Casillas may not be the most technically gifted custodian, but he has shown time-and-again that he has that most elusive and valuable quality in abundance - being in the right place at the right time.
First a heart-in-mouth moment for the Real defenders as opposition goalkeeper Butt headed narrowly wide from a corner, but, after watching that effort flash wide Casillas was called upon for four point blank saves.
A first save from Yildiray Basturk was superb, and the follow up from Berbatov was equally impressive.
As the black and red shirts poured forward, Casillas then had to save again from Berbatov, and clawed away a fourth shot to keep his side in front.
Aside from a Marco Van Basten volley ten years ago, the European Cup has never been won by a more fitting goal - and Real will know that in Zidane they purchased a man that won them the highest accolade in club football.
For a match summary from the game - click on the link below:
Real Madrid v Bayer Leverkusen
