The 19-year-old is the youngest player since start of the ATP Tour in 1990 to defeat three top-five players at the same event.
Alcaraz became the first player to beat Rafael Nadal and Djokovic at the same clay court event.
Three-time major winner Murray was set to face Djokovic for the 37th time in a highly anticipated clash on clay at the ATP Masters 1000 event in the Spanish capital.
The tournament will now take place on the Tennis World Tour videogame and run from April 27 to 30.
The Serbian will meet either five-time Madrid champion Rafael Nadal, the world number two, or Stefanos Tsitsipas in Sunday's final.
Rafael Nadal beat Stan Wawrinka 6-1, 6-2 to set up a clash with Stefanos Tsitsipas, who edged Alexander Zverev 7-5, 3-6, 6-2 in the other semi.