Novak is through to his first Masters 1000 semi-final in 2017.
The second seed advanced at the Mutua Madrid Open on Friday with a walkover, after no.6 seed Kei Nishikori withdrew from the event due to a wrist injury.
Novak, who won the title in Madrid in 2011 and 2016, will face Rafael Nadal (4) on Saturday for a spot in the final. The Spaniard toppled David Goffin in straight sets.
It will be the 50th career encounter between the two tennis champions, Djokovic leads 26-23 in their ATP H2H series.
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