The German, however, proved too strong, breaking five times for a 6-4 7-5 win on the main stadium hardcourt at Crandon Park.
"It's always good to have close sets, especially when you win them at the end. They give you confidence that you can go out in your next match knowing you can win close matches because you've just done it a day ago,” Kerber told reporters.
“You win the match, you're always happy about your performance.
Keys, in her second event since returning from wrist surgery, was the only seed to lose on Sunday, falling to 72nd-ranked Spaniard Lara Arruabarrena 7-5 7-5.
Third seed Halep took less than an hour to polish off qualifier Anett Kontaveit of Estonia 6-3 6-0 with an aggressive performance that left the Romanian very pleased.
"I think I played my best match of the year," Halep told the WTA. "I was confident, and knew what I had to do ... everything went pretty well for me tonight.
“I felt good when I came to site and was sure that it was going to come together because I work every day. At one point, it has to come.
"I felt the best that I have this year. I can move without pain or anything and I'm confident, which is the most important thing."
Russian seventh seed Kuznetsova, the runner-up last year, stayed on track for another tilt at the championship when she beat American qualifier Taylor Townsend 6-4 6-2.
A week after losing the Indian Wells final to compatriot Elena Vesnina, Kuznetsova’s stronger second serve proved the difference as she was broken just once while breaking her opponent four times.
The next challenge for 2006 champion Kuznetsova will be 11th seed Venus Williams, a three-time Miami champion, who was far too good for Romanian qualifier Patricia Maria Tig 6-3 6-0.
British 10th seed Johanna Konta and Australian 14th seed Sam Stosur also won their third round matches, Stosur earning a date with Halep.
(Reporting by Andrew Both in Cary, North Carolina; editing by Gene Cherry / Ian Ransom)
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