Kyrgios was battling with a hip problem throughout and required medical attention before the start of the second set.
He still managed to fashion eight break point opportunities but was held at arms length by his good friend Zverev whose stock continues to rise.
The German is 24-3 since the Munich Open in May and will face Kevin Anderson in the last eight; a rematch of their Citi Open final on Sunday.
Zverev breezed through that encounter in similar fashion to his victory here and he will be looking to extend his seven-match winning streak with Juan Carlos Ferrero on board. The Spaniard cast a watchful eye over proceedings on Court Central and his prodigy made a convincing start to the meeting.
He constructed a break point opportunity on Kyrgios’ opening service game and was finding great depth off his returns of the Australian’s domineering serve. However, that opportunity went amiss but he capitalized in the third game when he converted one of two break point chances with a stunning forehand return.
Kyrgios’ backhand had went AWOL and he was beginning to be afflicted by the same hip problem that has prompted retirements at his last three tournaments.
He has completed only two matches since his second round loss at the French Open but he was afforded an immediate route back into the set as Zverev served to consolidate the break. Instead the 20-year-old found a pair of supreme serves to keep his advantage intact.
He was similarly as cool at 4-2 when he gifted a pair of break back opportunities and he was serving for the opening set within 39 minutes.
The trainer was called for the Australian as he complained of a “sharp pain” and it was difficult to escape the feeling that Kyrgios may not complete this match.
He ambled back out for the beginning of set two and quick hold to 15 sharpened Zverev’s focus.
The set stayed on serve and Kyrgios’ penchant for approaching the net had the crowd on their feet; an impromptu down-the-line tweener just catching the outside of the sideline.
The crucial break then arrived in the fifth game when Zverev raised his level with a pair of stinging backhands. Kyrgios was regularly going to the serve and volley to shorten points but he miscued a volley on break point and Zverev had the finishing line in sight.
He held for 4-3 and was a pair of forehand errors away from breaking back but the German held his nerve before bringing up triple match point of the Australian’s serve.
He stamped his ticket with a backhand return winner.