Morata only signed for the Premier League champions on Friday but came off the bench in Singapore and set up Chelsea's second for Michy Batshuayi. Morata showed flashes of his ability, including one moment when he launched a Chelsea attack with a driving run through the heart of Bayern's midfield.
Chelsea were handed some sort of a lifeline when Nigeria worldwide, Victor Moses, provided an assist to Marco Alonso who scored late to make the first half end 3-1 in favour of Bayern Munich.
Muller was there, beating Cesc Fabregas to the ball to volley home and double the lead.
Rafinha put the German ahead before a Thomas Muller brace made it 3-0.
However, Chelsea fans on Twitter are far from upset after seeing promising youngsters Andreas Christensen and Jeremie Boga given a chance to impress against the Bundesliga champions.
But they were caught out of the blue by a belting strike from Rafinha on six minutes, the Brazilian right-back rifling the ball across Thibault Courtois and in off his right-hand post from 25 yards.
The final, taking place in Bayern's Allianz Arena, saw Chelsea become the first London side to win the Champions League when Drogba scored the winning penalty in the shootout.
It should have been 3-0 for the German giants and a hat-trick of assists for Ribery soon afterwards, but James Rodriguez shot over from close range.
Alvaro Morata made his Chelsea debut after coming on as a substitute in the 70th minute as he made his impact on the game nearly immediately.
Willian fired high before substitute David Luiz's long-range effort took a deflection and hit the post and fellow sub Fikayo Tomori headed a cross wide.
The Spain worldwide was introduced just after the hour and was able to flick Cesc Fabregas' corner into the path of Batshuayi to score with five minutes to play.
Rodriguez played his first full match since joining Bayern on a two-year load deal from Real Madrid and the Colombian winger was a constant menace to the Chelsea backline and unlucky not to open his account.