The Serbian had dropped the opening set against the 11th seed and received immediate treatment on the right arm he appeared to injure in his fourth-round meeting with Adrian Mannarino.
And, just two games after resuming play, Djokovic called an end to proceedings - meaning Berdych advances to his third Wimbledon semi-final 7-6 (7-2) 2-0, where Roger Federer awaits.
Djokovic’s withdrawal also ends his chances of overhauling Andy Murray in the ATP rankings. The Briton will remain world number one, despite his own injury-hit defeat to Sam Querrey on Wednesday.
Initially Djokovic did not appear to be hampered by the problem as the duo traded blows from the baseline in a tight set that advanced to a shootout without a single break point.
But the exertions soon began to take their toll on the three-time champion, who saw five points go to waste with unforced errors as Berdych pulled away, before another misstep handed the Czech the lead.
The second seed called for treatment straight away and underwent a medical time out, in an attempt to relieve pain on the elbow particularly.
It failed to have the desired effect, though, as Djokovic’s problems began to mount – his power noticeably dropping as Berdych served out to love in the opening game and then pounced on his opponent’s distinct lack of speed to break.
Only one more point was able to be played before Djokovic call a halt to proceedings, handing Berdych his last-four berth.
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