It means that the Spaniard remains on course to finally land his first ATP Masters title on hardcourt.
In the last four Nadal will take on the Russian Karen Khachanov , who beat Robin Haase of the Netherlands 6-3 6-1.
"It was a very important match for me," Nadal said.
"Being in the semi-finals is great news at the start of the hard court season, and winning three good matches in the first Masters 1000 is so important for me.
"He [Cilic] played unstoppable in the first set. But I resisted, I played with the right tactic and tried to find my solutions."
Stefanos Tsitsipas saved two match points to see off defending champion Alexander Zverev of Germany in their quarter-final contest, which ended 3-6 7-6 6-4.
The Greek teenager, who turns 20 on Sunday's final day, defeated his third straight top ten opponent at the tournament after knocking out Dominic Thiem and Wimbledon champion Novak Djokovic.
Tsitsipas is the youngest player to post three top ten wins at a single tournament since the 19-year-old Nadal at Monte Carlo in 2006. The Greek will take on Kevin Anderson for a place in the final.
South African Anderson beat Grigor Dimitrov 6-2 6-2.