The Japanese gave the German wildcard little chance to play his attacking game on the quick grass court and returned superbly in the second set.
"I am very satisfied with my performance today. It’s not easy to play Dustin and I did that very well today," Nishikori told reporters.
Brown, who upset Rafael Nadal at Halle last year, pushed Nishikori to 5-5 in the first set before the Japanese broke and then served out to take a 1-0 lead.
Nishikori then got to grips with his opponent's serve in the second set to move into the last eight of a tournament for the 10th time in 11 events this year.
Janowicz needed three sets to oust Colombian Alejandro Falla.
Italian Andreas Seppi continued his good run at Halle after beating local hero Tommy Haas on Tuesday, outmuscling Spain's Tommy Robredo 6-2 6-7(6) 6-3 to reach the quarter-finals at the tournament for the first time.
He will now meet France's Gael Monfils who beat Kazakh Mikhail Kukushkin in straight sets.
Robredo saved four match points before Seppi kept his cool and sealed the win at the fifth attempt after a lob by the Spaniard went long.
Top seed Roger Federer qualified for the last eight on Wednesday where he will face German Florian Mayer. Third seed Tomas Berdych meets Croatian Ivo Karlovic in the other quarter-final.
(Reporting by Karolos Grohmann; Editing by Toby Davis)
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