Roger Federer will meet Novak Djokovic in the final of the Indian Wells Masters.

World No.2 Novak Djokovic held on for a three-set win over American John Isner on Saturday to set up an Indian Wells Masters title showdown with Roger Federer.

Federer, a four-time champion in the California desert who is seeded seventh this year, was in dominant form in a 6-3 6-1 semi-final victory over Alexandr Dolgopolov.

Second-seeded Djokovic found the going much tougher against 12th-seeded Isner.

The towering 2.08m-tall American had beaten him in the semi-finals here in 2012, and gave the Serbian another scare before Djokovic pulled away in the third set for a 7-5 6-7 (2-7) 6-1 triumph.

Djokovic twice served for the match in the second set, at 5-4 and 6-5. But Isner held him off and won the tie-breaker, sealing it with an ace on his second set point.

But Isner was broken twice in the final frame, double-faulting to give Djokovic a 3-1 lead.

After another break for 5-1, Djokovic stormed home, winning every point of the final game with a service winner.

“Twice I had chance to finish it out and I played two bad games and he played an incredible tie-breaker,” Djokovic said.

“And, you know, when you get to the tiebreaker with John Isner, whoever you are, you’re not a favourite.”

The Serbian, who won the title here in 2008 and 2011, was pleased with how he regrouped.

“I didn’t let my concentration drop,” he said. “Already next point I was back in the game where I needed to be.”

On Sunday, Djokovic will face Federer for the 33rd time.

Federer’s slim 17-15 lead in their head-to-head includes a semi-final victory over Djokovic in Dubai last month.

The women’s final in the $US12 million ($A13.35 million) combined ATP Masters and WTA tournament – between world No.3 Agnieszka Radwanska and Flavia Pennetta – will also be contested on Sunday.

Federer, winner of a record 17 grand slam titles, will be going for a 22nd ATP Masters crown.

He thwarted world No.31 Dolgopolov’s bid to become just the sixth player to beat both Rafael Nadal and Federer in the same tournament.

Federer put 72 per cent of his first serves in play and didn’t face break point in an efficient display before an adoring crowd at the Indian Wells Tennis Garden’s stadium court.

“It was one of my best serving days ever,” he said. “When you are serving like that, everything seems easier. I was just going for it out there.”

Federer seemed untroubled by the breezy conditions, and once he’d gained the first service break of the match, for a 5-3 lead in the first set, he was hardly troubled by Dolgopolov.

Federer broke Dolgopolov in the opening game of the second set, and held at love with one of his seven aces on game point for a 2-0 lead.

By reaching the semi-finals, Federer is assured of returning to the top five in the world rankings for the first time since last September.

If he wins a fifth title to go with those he captured in 2004, 2005, 2006 and 2012 he’s projected to rise to number four in the world.