The Japanese world number eight looked in trouble when he faced a break point at 3-3 in the deciding set but he finished fast to register his first win in Stan Smith Group.
"I got a bit lucky in the last couple of games but I worked really hard today," the 25-year-old, who reached the semi-finals on his debut at the tournament last season, said on court.
A match full of powerful baseline rallies ebbed and flowed.
World number six Berdych, who was beaten by Roger Federer in his opening match, squandered a great chance in the first set when Nishikori was serving at 4-5 15-30, missing a wide-open court with a backhand at the end of brilliant rally.
It proved costly as Berdych dropped serve in the next game and Nishikori clinched the set on serve with a pinpoint forehand winner past the wrong-footed Czech.
Nishikori went 2-0 ahead in the second set but Berdych reeled off five games in a row with some thunderous winners to turn the match around and send it towards a deciding set -- the first so far in the singles this year at the O2 Arena.
An engrossing third set reached a crucial juncture at 3-3 when a lucky net cord gave Berdych a break point, but Nishikori showed great defensive skills to fend off a big attack from his Czech opponent and kept his nose ahead at 4-3.
Two forehand errors from the Berdych racket allowed Nishikori to move 5-3 ahead and the Japanese player secured victory with a love hold.
Defending champion Djokovic will qualify for the semi-finals with a match to spare if he beats Roger Federer later on Tuesday while Federer will progress if he wins in straight sets.
(editing by Justin Palmer)
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