A five-time Indian Wells champion Roger Federer couldn't finish his second round match against Federico Delbonis on Saturday night, leading 6-3 2-2 before the rain halted the action and send it to Sunday.
It was another snag in the return for world number 13 Djokovic, who admitted he lacked composure while playing in just his second event of 2018 and first since having surgery.
"It felt like first match I ever played on the tour", Djokovic said. I just completely lost rhythm, everything.
"I was grateful to be out on the court after surgery that quickly, but at the same time, I just didn't feel good at all". After handing back an early break to allow Krajinovic to draw level at 2-all, the defending champion moved into cruise control.
Still, Chardy is no longer the top-30 player he was a few years ago, and he's trying to find his form after some wild inconsistencies. "But I recovered very quickly, and I got myself ready", he added.
Djokovic underwent right elbow surgery after falling in the fourth round of the Australian Open in January.
The 34-old, who has seven career titles, pounded down 12 aces, including six in the deciding set.
On a day when several seeds fell, the Serbian's loss and Zverev's departure at the hands of Joao Sousa were the biggest surprises.
Federer improved to 65-5 since returning from a left knee injury last year with his third-round victory in a rare day match.
"I was feeling like he was not loving my slice and I was also mixing in dropshots", said Federer who extended his perfect record this season to 14-0.
"I think really I was able to mix up my game nicely, make it difficult for him there".
Djokovic revealed his underwhelming performance on Sunday was more of a mental issue than anything else. In other men's matches, American Taylor Fritz defeated Fernando Verdasco, of Spain, 4-6, 6-2, 7-6 (7/1), Croatia's Borna Coric breezed past Roberto Bautista 6-1, 6-3 and Pablo Carreno-Busta, of Spain, stopped Russian Daniil Medvedev 6-1, 7-5.
Djokovic will now be hoping for a better showing at the next ATP Masters event he is scheduled to play in a few days time, the Miami Open.
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