Nadal is now out with a recurrence of his hip injury, Djokovic is struggling after elbow problems and Murray is recovering from major surgery in January.
Djokovic bowed out to South Korean Chung Hyeon in the fourth round of the 2018 Australian Open.
Rain barred Federer from completing the first match of his title defence at the season's opening ATP Masters 1000 tournament on Saturday.
Gael Monfils upset number 15 seed and 2012 runner-up John Isner 6-7 (5), 7-6 (3), 7-5.
Daniel, speaking on the biggest win of his career, said, "It's kind of hard to describe.I can't believe I beat someone like that on the center court like this; it's insane".
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With two titles at St Petersburg and Doha and a 14-match winning streak, World No. 9 Petra Kvitova was one of the biggest contenders for the women's title. "Very weird", Djokovic said.
Djokovic's performance in the final set against the world's 109th-ranked player on center court raised some eyebrows, with four-times grand slam champion Jim Courier saying the Serb had "capitulated".
In other men's matches, Juan Martin del Potro steamed his way into the third round as the sixth seed needed just 69 minutes to beat Australian teenager Alex de Minaur 6-2, 6-1.
Playing for a third consecutive day due to weather delays, the 36-year-old Swiss showed no sign of wear en route to a 6-2, 6-1 thrashing of the Serbian in the pair's first ever meeting. So it was definitely nerve-wracking kind of, but I was enjoying it so much out there and I was playing my best. Ninth seed Lucas Pouille was beaten by Indian qualifier Yuki Bhambri.
A five-time victor at Indian Wells, Federer needed less than an hour to crush Krajinovic.
The win sets up a third-round showdown with Spaniard David Ferrer, who defeated Tennys Sandgren of the United States 6-2, 7-6 (7-3).