The former UFC heavyweight champion forced Kharitonov to the ground and submitted him at 4:28 of the first round.
Barnett will face Daniel Cormier for the championship. No date has been set, but the final is expected to happen in early 2012.
"Cormier is a great opponent," Barnett said. "He's a guy who has competed at the highest level of athletics.
"He's going to be much tougher than these [previous] guys."
Barnett defeated Brett Rogers in the opening round of the Grand Prix. His win over Kharitonov improves his professional MMA record to 31-5.
Kharitonov, who brought a two-fight win streak into the bout, slips to 18-5.
Cormier cuts down 'Bigfoot' with right hand
Experience and size were supposed to be Daniel Cormier's Achilles' heel against Antonio Silva.
But Cormier quickly nullified those disadvantages with speed and punching power to register a first-round knockout in a Strikeforce Heavyweight Grand Prix semifinal bout.
Cormier is a supremely skilled wrestler, but it is his stand-up skills that have many speaking of him as a future heavyweight champion. And he displayed his improved stand-up striking skills against Bigfoot.
He dropped Silva early in the first round with a hard overhand right. Cormier would floor Silva with the same punch later in the round.
The finishing touches would come with a little more than a minute remaining in the opening stanza.
Cormier connected with a stiff left jab that stunned Silva then followed it up with a right uppercut. Silva fell and the fight was stopped at the 3:56 mark.
"It was great," said Cormier, who was added to the Strikeforce GP when Alistair Overeem pulled out due to injury. "I fought one of the top-five heavyweights and knocked him out.
"Guys, I'm going to the final and I'm winning that title."
Silva, who entered the fight ranked fifth in the ESPN.com heavyweight power rankings, fell to 16-3. Cormier improves to 9-0.
Rockhold captures middleweight title
The 26-year-old who had been out of action for 19 months upset Souza by earning a unanimous decision.
The judges scored the fight 50-45, 48-47 and 48-47. ESPN.com had it 48-47 for Rockhold.
"It's amazing," said Rockhold, who entered this 185-pound title bout having never lost in Strikeforce. "I couldn't do this without so many people in my corner."
"I got rocked a couple of times, but I won the fight. People doubted me, but I have one of the best camps [American Kickboxing Academy] around me."
Rockhold (8-1) took the title by handling Souza on the feet. The southpaw continuously landed right-left combinations and tossed in several kicks that found their marks.
Souza (14-3, with one no contest) not only lost his title, but all the momentum he'd garnered from a four-fight win streak in Strikeforce.
Lawal KOs Gracie in first
Former Strikeforce light heavyweight champion Muhammed Lawal returned to action for the first time in more than a year and went home an impressive winner.
Lawal did not show much respect for Gracie's stand-up skills, keeping his hands low. It didn't take long before he got Gracie's attention with straight jabs and a few kicks.
An overhand right from Lawal found Gracie's chin and the jiu-jitsu specialist went down immediately. Gracie never recovered and was spared further punishment at the 4:33 mark.
Lawal improved to 8-1, while rebounding from his title loss to Rafael Cavalcante in August 2010. Gracie, who started his MMA career on a four-fight win streak, suffered his first loss.
Healy submits Blanco
Lightweight Pat Healy handed Maximo Blanco the first submission loss of his professional career.
Blanco, who was making his Strikeforce debut, got caught in a rear-naked choke in the second round and tapped at the 4:24 mark.
The win was Healy's third in a row and boosted his record to 26-16.
Blanco (8-3-1, one no contest) entered the bout on a six-fight win streak.
Franklin McNeil covers mixed martial arts and boxing for ESPN.com. Follow him on Twitter at www.twitter.com/Franklin_McNeil.