Tomas Berdych is into the last four at The Championships after Novak retired with an elbow injury early in the second set.
Three-time former champion beat Adrian Mannarino 6-2, 7-6 (5), 6-4 to move into his ninth Wimbledon quarter-final.
Three-time former champion booked his place in the Wimbledon last 16 with a comprehensive 6-4, 6-1, 7-6 victory over Ernests Gulbis.
Nole will play in his fourth Wimbledon final on Sunday after he beat no.21 seed Richard Gasquet 7-6, 6-4, 6-4 in two hours and 21 minutes.
Novak's straight sets win over ninth seed Marin Cilic earned him his 50th career victory at the All England Club. He will face Richard Gasquet on Friday.
Top seed lost first two sets but fought back to beat Kevin Anderson 6-7 (8), 6-7 (8), 6-1, 6-4, 7-5 and reach the last 8.