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The 52-minute "doule-bagel" was the first for the Serb at the elite ATP level, bettering his 6-1, 6-0 win over Argentina's David Nalbandian in the Queen's Club semi-finals in 2008, a rout which took four minutes less.
Djokovic also defeated Britain's Andy Murray by the same scoreline in Miami two years ago.
"I played enough to win, I had great service games and on his serve I never felt pressure. He didn't put up much of an effort. Anytime you win like this the opponent has to be playing really poorly," said the world No. 4.
Second seed Djokovic saved three break points in the first set before stepping on the gas against a 59h-ranked opponent who had claimed his first victory since the US Open in the first round here.
Hernych's cause was not helped by committing 40 errors in the loss.
Djokovic improved to 68-18 on the season as he awaits an opponent from Swiss sixth seed Stanislas Wawrinka and Finn Jarkko Nieminen and he feels he is currently on course to reach the weekend final.
Evgeny Korolev will line up against Roger Federer in the last eight after defeating Jeremy Chardy 6-4, 7-6 (7/1), a day after the Frenchman fired 24 aces to humble James Blake.
Swiss Marco Chiudinelli kept national hopes high as he beat qualifying compatriot Michael Lammer 2-6, 6-3, 6-3, firing eight aces and breaking three times.
The result marks the second quarter-final in six weeks for the Swiss after a similar performance in Bangkok.
Chiudinelli improved to 9-11 this season and will face the winner from France's Richard Gasquet and American John Isner.