The 31-year-old Czech looked comfortable after easing through the first set, but Nishioka fought back to claim a 1-6 7-6(5) 6-4 triumph.
It took just half an hour for Berdych to take a one-set lead, and he required just one more game on the board after going 5-2 up in the second following a double break.
However, Nishioka was not done as he claimed a double break of his own before snatching the tie-break 7-5 after just over an hour.
Berdych was stunned by his Japanese opponent's comeback and it showed in the third set when he lost his first two service games.
The 2010 Wimbledon finalist was unable to recover as Nishioka grabbed a place in the next round.body check tags ::