The 54-year-old German was jailed for two years and six months by a London court on Friday for hiding hundreds of thousands of pounds of assets after he was declared bankrupt.
"Just heartbroken, I mean, for him. He's a friend, long-time friend, a coach for three, four years, someone I consider close in my life and has contributed a lot to my success in my career," Djokovic told reporters at the Madrid Open.
The pair worked together between 2014 and 2016, with Becker guiding Djokovic to six of his 20 Grand Slam titles.
"I just hope he will go through this period... and when he comes out he's able to live his life as, I don't know if we'll use the word 'normal', because the life is definitely changing, I mean, for anybody going to prison," added the Serbian.
"I just pray for him. I hope things will be well in terms of his health, his mental health, because that's going to be the most challenging part."
Djokovic, a three-times winner at the ATP Masters 1000 event in Madrid, is looking for his first title of the season after losing to Andrey Rublev in the final of the Serbia Open last week.
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Boris Becker was an incredible talent (as a player, pundit and coach)....however ultimately for reasons of arrogance and naivety he is where he is...and he has brought this situation on himself....protestations from the likes of Novak Djocavic are of absolutely no value when we consider his own record towards authority,....what international players must realise (and in all fairness I think the most do) is that you have amazing talent, amazing earning potential, but you have no right to abuse your position in the worlds of global economics and politics