"He has surgery of both hips today and tomorrow, so that's unfortunate. He couldn't come, he was supposed to come here," Djokovic said during a pre-tournament news conference.
"Basically in the finals of Indian Wells he called us and said that he had an emergency and he has to operate both hips."
While Becker recovers, world number two Djokovic arrives in Miami fresh off a confidence-boosting win over Roger Federer in Sunday's final of the BNP Paribas Open in Indian Wells.
It was the first win of the season for the Serb, who joined forces with the German tennis great last December after losing grand slam finals in 2013 to Spain's Rafa Nadal (U.S. Open) and Briton Murray (Wimbledon).
"I knew I'm playing well," said Djokovic, who will take on Frenchman Jeremy Chardy in a second-round clash after receiving a first-round bye. "I had an incredible end of 2013, so I did have confidence but I started a little bit doubting myself on the court.
"I was struggling a little bit with my, I would say, consistency and the concentration."
Djokovic expects Becker to be back with his team in Monte Carlo next month and otherwise expects no other disruptions to their schedule.
While Djokovic and Becker will continue their relationship, defending champion Murray will go it alone in Miami, announcing this week that he had split with Ivan Lendl.
Murray, the world number six, offered few clues on Thursday as to why he and Lendl ended their successful partnership but reiterated that it had been a mutual decision.
"Well, to be honest, I was not surprised," said Djokovic, when asked for his thoughts on the breakup. "But, again, I didn't know what to expect.
"They worked for two years, and obviously it brought both of them, especially Andy, a lot of success on the court.
"He won Olympic Games, won a few grand slams. I think it was a very good decision from inside to be working with Ivan.
"Now they split. I mean, they obviously had a good reason for that. I'm not the one who should judge."
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