The 20-year-old German is looking to win the third Masters event of his career and advanced to a last-eight showdown against Croatia’s Borna Coric, who ended the run of Canadian prospect Denis Shapovalov 7-6(2) 4-6 6-4 in a tight encounter.
The fourth-seeded Zverev had battled through a pair of three-set wins in his opening two rounds but was keen to make short work of Kyrgios when he broke serve in the first game and stormed to a 5-1 advantage.
The 22-year-old Kyrgios battled back to win three straight games to make it 5-4 but Zverev held his nerve and serve to close out the opener in 34 minutes.
Kyrgios, who had reached the Miami semi-finals in the previous two years, saw his hopes of at least matching that feat evaporate in the second set after his opponent secured the only break in the fifth game and rode it out for a well-earned win.