With temperatures at Indian Wells in excess of 105 degrees, Evans broke in the opening game but world number five Nishikori hit back immediately and captured the set in 42 minutes.
Breaks were traded again at the start of the second before Nishikori sealed the match in an hour and 24 minutes.
Kyle Edmund is also out, 6-4 7-6 (7-5) to defending champion Novak Djokovic.
Following the surprise defeat of world number one Andy Murray at the hands of qualifier Vasek Pospisil the previous evening, Evans, 26, produced a spirited performance, but some pinpoint accuracy from Nishikori saw him break again in game eight of the first set.
World number 41 Evans, who beat Dustin Brown in the previous round, continued to frequently match the quality of his Japanese opponent's groundstrokes but gradually faded as the assured Nishikori moved through to face Gilles Muller of Luxembourg in round three.
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British number two Dan Evans was beaten 6-3 6-4 by Japan's Kei Nishikori in the second round of the BNP Paribas Open.