The German replaces American Serena Williams.
Surpasses Jimmy Connors as tournament's oldest winner
For Kuznetsova, it was a third disappointment in as many finals at Indian Wells.
They met most recently at the Australian Open semifinal, where Federer prevailed in five sets.
The Scot will be replaced in the main draw by American world number 136 Taylor Fritz.
Kyrgios withdrew from their highly anticipated quarterfinal with food poisoning.
The Swiss will meet 21st seed Pablo Carreno Busta in the last four.
The Australian ended three-time defending champion's 19-match winning streak in the first Masters tournament of the year.
The match will be a reprise of the Australian Open final in January.
Wawrinka had it easy against Kohlschreiber while Kerber battled past Parmentier.
Djokovic now has a tough third-round clash with former US Open champion Juan Martin del Potro.
The world No.1 was again brought up short in Indian Wells, where his best showing is a 2009 runner-up finish to Rafael Nadal.
QATAR’S Rashid Nawaf beat Uzbekistan’s Rasul Nurmukhamedov 6-2, 6-0 to clinch the Asian Junior (Under-14) singles title at the hard courts of Khalifa International Complex last week.