Federer quickly retreated to the baseline, unaware of his 6-3 7-6(4) triumph, while a confused Nishikori approached the net to shake hands much to the amusement of the German crowd.
"It was the first time in my career in over a thousand matches," a bemused Federer said of his faux pas after he set up a final with Colombia's Alejandro Falla
World number 69 Falla overcame home favourite Philipp Kohlschreiber 5-7 7-6(5) 6-4.
Federer, chasing his seventh trophy in Halle, fired 10 aces against Nishikori.
The Japanese fourth seed offered some resistance in the second set, forcing a tiebreak that he led 4-2, but the Swiss capitalised on some wayward hitting to win five points in a row and ease to victory.
Falla needed two hours 21 minutes to defeat German Kohlschreiber.
Having lost the first set Falla, who has not beaten Federer in six attempts, fought back superbly against a player ranked 42 places above him to steal the next two sets and reach the second final of his career.
"I'm absolutely delighted. It was a very hard match," Falla told reporters.
"I've always had to work hard this week because I've fallen behind in every match. But grass is my favourite surface and I've got a chance against anybody on here."
(Reporting by Michael Hann, editing by Tony Jimenez and Pritha Sarkar)
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