Kuznetsova played exceptional defence and used her strong serve and a varied groundstroke attack to edge third seed Karolina Pliskova 7-6 (7-5), 7-6 (7-2) in a tense showdown following Vesnina's 6-3, 6-4 win over Kristina Mladenovic.
Mladenovic, the 28th seed, continued an impressive run of form beating 13th seed and 2011 victor Wozniacki 3-6, 7-6 (4), 6-2 to reach her first Premier Mandatory semifinal and guarantee her debut in the Top 20 in next week's WTA rankings.
Vesnina dominated again at the start of the second set, breaking Mladenovic's first two service games in building a 5-1 lead.
A third set that, like the first two, featured multiple service breaks came down to marathon ninth game, in which Kuznetsova saved four break points before Vesnina converted her fifth with a stinging service victor to find herself serving for the match.
"I'm playing great tennis and I didn't expect it because I'm still on the comeback", said Federer, who won his record 18th Grand Slam title at the Australian Open in January after being sidelined by various injuries for much of 2016.
Vesnina, 30, was playing in her first final at a "Premier Mandatory" event - those at Indian Wells, Key Biscayne, Madrid and Beijing.
In a major setback, seven-time Grand Slam champion Venus Williams suffered a crushing defeat against World No. 15 Elena Vesnina to bow out of the Indian Wells Masters under the lights of Stadium 1 on Thursday evening.
Like Kuznetsova, Vesnina has faced four fellow seeded opponents on her way through to the biggest singles final of her career. I played her a few times, and different conditions twice.
"I guess I'm on fire", Vesnina said.
World No 8 Kuznetsova will make her third appearance in the Indian Wells final after finishing runner-up in the tournament in both 2007 and 2008. "I am looking forward to having a great game and may the best win".
The final shot sailed past the baseline and Elena Vesnina crumpled to the court in exhilaration.
Nishikori had not dropped a set in the tournament until losing the first against Sock.
Vesnina had 46 winners and 49 unforced errors. However, Vesnina's two title triumphs came in 2013 at the global tier event in Hobart against Mona Barthel, and a Premier-level title on the grass courts of Eastbourne in 2013, dispatching Jamie Hampton.
"I didn't break her when I had the opportunity", Wozniacki said.
Throughout the match, the three-time finalist answered adversity with proactive play.
"I needed a match like this".
Third seed Wawrinka, who six months ago beat Novak Djokovic to win the US Open, won a gripping slugfest against the 23-year-old Austrian, hammering home five third-set aces including one to reach quadruple match point in the tiebreak.
Kuznetsova lost in the final for the time.