The Serbian was taken to four sets by Frenchman Enzo Couacaud, with the injury proving difficult to overcome at times.
Djokovic could be seen limping after points and took a second-set injury timeout for treatment from his physio.
And with a third-round match against Grigor Dimitrov to come on Saturday, Djokovic admits he is concerned by his condition.
“It’s not good at all, to be honest with you,” said the nine-time winner at Melbourne Park. “I’ll take it day by day.
“It was better in the last match than tonight, to be honest. That’s all I can say now.
“I just need God to help me now, and the physio and everyone. I’ll take it day by day and hopefully, I’ll be able to recover for a tough match-up in the next round.”
Djokovic was also challenged mentally with fans heckling him at Rod Laver Arena, forcing the 35-year-old to demand chair umpire Fergus Murphy remove the “drunk out of his mind” fan.
“The guy is drunk out of his mind,” Djokovic told Murphy. “From the first point he’s been provoking me. He's not here to watch tennis, he just wants to get in my head, you heard him at least 10 times, I heard him 50.
“What are you going to do about it? Get him out of the stadium.”
Djokovic gave credit to Couacaud but, despite enjoying the night session, pointed out that the atmosphere became too “negative”.
“It's expected when you walk on the court as a favourite,” Djokovic said of the match. “Somebody playing his first time on Rod Laver Arena, you have to adapt and accept it.
“It had a little bit of everything tonight. I’m glad to get through this kind of match in four sets. I wanted to get through in three but credit to him, he played really well in that second set.
“It was interesting circumstances to deal with but that’s a grand slam - the atmosphere was electric but in a bit of a negative way.”