The pair will meet in the quarter-finals on Wednesday after wrapping up last-16 victories within seconds of each as the light faded on Monday. Djokovic defeated Tommy Haas in straight sets, while Berdych needed four to see off a battling Bernard Tomic.
It means Djokovic and Berdych will face off again, just as they did in the semi-finals three years ago, a match won in straight sets by the Czech.
Djokovic has improved immensely since then though and he will go into the clash as a hot favourite.
The Serb did not appear to be at his best during a 6-1 6-4 7-6 (7/4) victory over the 35-year-old Haas, who was looking to become the oldest player since Tom Okker in 1979 to reach the last eight.
However, he was more than happy with his form after the contest.
"I think I am playing really, really good tennis at this moment, better than in 2011 when I won it, so I feel confident," said the world number one.
A repeat of Haas' victory over Djokovic in Miami earlier this season never looked on the cards.
Some sloppy tennis from Haas in the early stages gave Djokovic a flying start but the world number one then dropped his serve for the first time in the tournament in the fifth game of the second as he was made to fight harder.
He recovered from 2-4 to take the second set but the trick was repeated in the third, Haas breaking serve as Djokovic tried to close out the match.
With the light fading and quality of the tennis having improved substantially, Djokovic must have been concerned as he headed into the tie-break but he was 5-1 up at the change of ends and finished things off soon after.
"It was always going to be tough,'' said Djokovic. "I had a bad record against him.
"I lost twice in 2009 against him. He is a grasscourt specialist, he has a great variety in his game, so it was a tough challenge for me but I played really well.
"It was never going to be easy, I knew he would improve. He missed a lot of easy shots in the first.
"I had to work and I was serving well, returning exceptionally good in important moments.
"It was a minor setback at 5-3, I was 30-0 and made a couple of double faults but I am glad I closed it out.''
Over on Court One, Berdych had a tougher time of it against Tomic, a player who has not exactly been known for his fighting qualities in the past.
However, he stood toe to toe with Berdych for much of their last-16 clash, one which lasted just shy of three hours.
Berdych wrested control by taking a crucial third set and an early break of the Tomic serve in the fourth was grasped tightly for the remainder of the contest as the 2010 runner-up secured a 7-6 (7/4) 6-7 (5/7) 6-4 6-4 victory.
Earlier, Juan Martin Del Potro set up a quarter-final clash with David Ferrer.
Del Potro was the more impressive, holding serve through his straight-sets win over Andreas Seppi.
However, Ferrer, ever the battler, showed his fighting qualities by coming from behind to beat Ivan Dodig in four sets.
Del Potro emerged from his clash with Italian Seppi as a 6-4 7-6 (7/2) 6-3 winner.
Seppi created just two break points - one in the first set, one in the third - and could take neither on Court One.
Del Potro got 72 per cent of his first serves in play and will likely need to serve well again on Wednesday against Ferrer as the Spaniard has beaten him in each of their last four meetings, including a straight-sets success in a last-16 clash at the All England Club last season.
Ferrer, beaten by Andy Murray in the last eight 12 months ago, was tested for the first two sets by Dodig but once he had squared the match he pushed on to secure a 6-7 (3/7) 7-6 (8/6) 6-1 6-1 win.
Dodig, who has enjoyed some impressive results on grass of late, was left regretting not being able to clinch the second set. Serving at 6-6 in the tie-break he was within touching distance of a two-set lead.
However, Ferrer won the next two points to level the contest and after that the Croatian looked mentally spent.
Another Spaniard, Fernando Verdasco, also progressed to the last eight thanks to a straight-sets win over Kenny de Schepper.
De Schepper had beaten seed Juan Monaco in the previous round but he had no answer to Verdasco and went down 6-4 6-4 6-4.
Verdasco meets Briton Murray next.
Meanwhile, big-serving Jerzy Janowicz stayed on course for a semi-final clash with Murray by edging past Jurgen Melzer.
Janowicz needed five sets to see off his Austrian foe but came through to set up a quarter-final clash with fellow Pole Lukasz Kubot.
Janowicz who blasted 30 aces past Nicolas Almagro in his previous match did not find things so easy against Melzer. Just 16 aces resulted in five sets before he managed to secure a 3-6 7-6 (7/1) 6-4 4-6 6-4 victory.
The 22-year-old is regarded by most as the biggest danger to Murray in the botttom half of the draw.
He beat the British star en route to the final of last year's Paris Masters, a run which made him one of the players to watch in 2013.
Meanwhile, Kubot banged down 24 aces as, like Janowicz, he made the quarter-finals of a Grand Slam for the first time.
Ranked a lowly 130th in the world, Kubot also had to come from behind to defeat Frenchman Adrian Mannarino 4-6 6-3 3-6 6-3 6-4.