Cilic was the second higher-seeded player to lose to 15th-seeded Goffin, who upset No. 3 Stan Wawrinka in the fourth round. Cilic lost to Goffin nearly two weeks ago on clay in Belgium during first-round Davis Cup play.
Goffin needed a third-set tiebreaker to beat Wawrinka after the 25-year-old Belgian served for the match at 5-3 in the second and third sets. The 10th-seeded Cilic fell to 0-8 in quarterfinals at Masters 1000 events.
Goffin, a slender 5-foot-11, withstood the power of Cilic, who is 6-6 and outweighs Goffin by 46 pounds.
"I knew that on my serve I had to battle to win every service game because sometimes he can serve bombs and in 10 seconds can win his games," said Goffin, who fell down at 5-4 in the first set.
"It was just bad for me, but at the end I stayed focused in the tiebreak. It was the key of the match to win the first set and be more relaxed in the second to play much better."
"It's good in tennis that you don't have to be big or a tall guy to be good. Otherwise I had no chance to get in the top 20," said Goffin, ranked 18th. "Maybe I'm quicker. I can take the ball earlier than a big guy. Of course I don't have a big serve. I have other weapons. That's why tennis is a nice sport."
Victoria Azarenka shut out Magdalena Rybarikova 6-0, 6-0 in 67 minutes to reach the women's semifinals. She will play Karolina Pliskova, who beat 18-year-old Russian Daria Kasatkina 6-3, 6-2 in an hour.
Azarenka broke Rybarikova six times and connected on 60 percent of her first serves. Rybarikova had 25 unforced errors and just nine winners. After losing the first set, she took a medical timeout to have her upper thigh taped heavily.
Azarenka has dropped one set in four matches so far; when she won Indian Wells in 2012, she also dropped just one set. She has won 11 of 12 matches this year.
"Confidence for me this year comes from being very well prepared and feeling healthy," she said. "What I want to do on the court is apply things I have been working on on the practice court and bring it to the matches because I feel that was going to push me to get better results."
Pliskova had 30 winners and 10 unforced errors. She fired nine aces and won all six of her points at net.
"(I'm) happy also for the doubles (win), because it's one of the biggest tournaments in the world," Pliskova said. "It's my first biggest final in the doubles, and especially happy to be there with my partner Julia."
Pliskova ended last year at a career-high No. 11 in the WTA rankings. Her semifinal singles showing here is her first at a Premier Mandatory event.
"I played some good tennis this week, and especially there is Miami (next week)," she said, "and so I have chances to go and improve the ranking and get close to top 10 again."