He was thus on the verge of losing officially for the third time since the U.S. Open, a result that would have dampened a season that for a while threatened to be the best ever in the men's game. Prior to August, he tasted defeat once, courtesy of Mr. Federer.
If only slightly, it would have given his rivals, Berdych and Roger Federer included, more hope for the rest of the tournament and into 2012.
But guess what?
Djokovic and his ailing shoulder hung in there, and the Serb eked out a 3-6, 6-3, 7-6 (3) victory, saving a match point in the process, to give Group A some semblance of normalcy. Earlier in the day, David Ferrer disappointed the locals by overcoming a wonky Andy Murray in straight sets.
When Djokovic said after his win that he hung in there, it was more than a cliché. For most of the 2-hour, 40-minute affair he was on the back foot, playing defense. It wasn't the explosive Djokovic that combined attacking with retrieving.
All eyes were on Djokovic's right shoulder, and in a sign of things to come, he double-faulted on his first service point. He shook his shoulder midway in the first set, trying to loosen it up, but it never really got going.
Djokovic lost as many points as he won on serve (13) in the opening set, and how he managed to improve the numbers was a mystery because his serve speed remained low. The one thing he did do was boost his first-serve percentage in the second, taking the pace off.
"I might have been a favorite on the paper, but I knew that the chances are more or less the same for both of us to win tonight because I haven't been playing my best in maybe month and a half," said Djokovic, who registered his 70th win of 2011.
Berdych was eager to pounce on the second serve, yet as the final set wore on, he was too aggressive, often missing.
If Djokovic's serving woes were caused by his shoulder, inactivity is likely to blame for his subpar (for him) returning. Berdych's first-serve percentage ended at 46, yet he was still able to push Djokovic to the limit.
More than once Djokovic became annoyed when he missed a second-serve return.
Djokovic, though, didn't miss when it really mattered, and perhaps that shouldn't be a surprise. Only the cool Swede, Bjorn Borg, has a higher winning percentage, if the TV stats men are to be believed, in decisive sets (as in, the third set in a three-set match and fifth set in a five-setter).
Berdych, who toppled Djokovic at Wimbledon last year on his way to the final, was the one erring, and with the forehand. One sailed into the net, wildly, with Berdych holding match point at 6-5 in the third, and he coughed up five unforced errors on that wing in the tiebreaker.
"I don't know what I can take positive from this game," Berdych said. "I mean, probably could be something. But the first thing is going to be definitely to start to forget it as quick as possible and be ready for Wednesday."
You get the sense Djokovic, coming off an emotional win, will be difficult to stop Wednesday evening when he tangles with Ferrer.
London-based Ravi Ubha covers soccer and tennis for ESPN.com. You can follow him on Twitter.