Two-time defending champion Alcaraz crashes out in Madrid
He was also on a four-match losing streak heading into the Madrid Open.
All that seemed like a distant memory in the quarter-finals against Alcaraz as Rublev maximised on his powerful brand of tennis to shock the Spanish world number three and reach the semi-finals at a seventh different Masters 1000 tournament, from a full set of nine.
Alcaraz missed the clay-court tournaments in Monte Carlo and Barcelona last month due to a forearm injury and needed a third-set tiebreak to squeeze past last year's finalist Jan-Lennard Struff in the Madrid fourth round on Tuesday.
He couldn't hold off an inspired Rublev though, his quest to become the first man to win three consecutive titles in Madrid coming to a crashing halt.
"I think the serve saved me a lot of times today but I think the key was that I think it was one of my first matches that I was completely calm all the match, I didn't say one word, even if I was losing," said Rublev, who now owns at least one victory against each of the current world's top 10.
"I think that was the key also that I was able to serve even better with the time."
Alcaraz played a convincing first set, breaking serve in the fifth game en route to a 41-minute lead.
Rublev was 0/5 on break points before he finally converted his first one to open up a 3-0 gap in the second set. Despite an argument with chair umpire Fergus Murphy over a challenge request that was cancelled when Rublev rubbed off the mark with his foot, the Russian kept his cool to serve out the frame and force a decider.
Two breaks of serve gave Rublev full control of the final set and he finished the match in just under two hours, firing 30 winners along the way.
He awaits Taylor Fritz or Francisco Cerundolo in the final four.
Earlier on centre court, Elena Rybakina battled back from 2-5 down in the deciding set and saved two match points to overcome Yulia Putintseva 4-6, 7-6 (7/4), 7-5 and reach the semi-finals of the WTA event.
Fourth seed Rybakina produced key serves to swat away two match points at 2-5 and broke Putintseva as she was serving for the victory at 5-3.
In the first all-Kazakh quarter-final at this level on the women's tour, Rybakina lacked efficiency on her break point opportunities, converting just three of 12 chances, and struggled to deal with Putintsev's deft drop shots.
But a late-match collapse from Putintseva, who smashed her racquet and left it on court after the match, helped Rybakina advance to her sixth semi-final of the season, where she will face defending champion Aryna Sabalenka or 17-year-old Mirra Andreeva.
Rybakina owns a tour-leading 30 wins in 2024, and has been successful in her last 12 deciding sets this season.