Little separated both players in the early stages of the third set, but a pair of forehand errors from Berdych gifted Federer a break to lead 4-2.
"I felt like I was in control and I was able to generate more chances than he did", Federer said.
"I completely went down physically and mentally, and also my tennis was completely out", Wawrinka said. I'm going to serve big and play big. "It was really humid, not easy to play some great tennis".
The Swiss maestro survived two match points before beating the Czech in the third-set tiebreak, digging deep from his reservoir of skill, poise and experience toto move to the semi-final stage. Three Americans left in the draw, including a highly ranked Jack Sock, and unseeded Donald Young and Jared Donaldson all have matches in the Grandstand as well, starting at 10:50 a.m.
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Berdych served for the match at 6-4 in the tiebreak but Federer reeled off four points in a row, including two unplayable serves, and secured the win when the 10th seed crumbled with an bad second serve. She'll next face 12th-seeded Caroline Wozniacki, a 6-4, 6-3 victor over unseeded Lucie Safarova.
"I tried to stay calm and focus again", said Nishikori, regarding the loss of the second set. I feel like I earned it more. Wozniacki, the 12th seed, took that set over the sixth-seeded Muguruza 7-6 (1).
Bautista Agut played the match of his life, hitting the ball deep with relentless precision in an effort to keep Federer pinned to the baseline, giving the 18-times grand slam champion everything he could handle.
Federer is now 4-0 in tiebreakers at this tournament, none of the first three as pressure-packed as the one against Berdych. The Czech player is down 6-17 in the head to head against Federer, who lost to Berdych last time four years ago in Dubai.
ATP Miami: Roger Federer wins Miami title to complete hard court sweep
But then Federer got the break he needed in the eighth game of the first set, went ahead 5-3, and held on to win the set 6-3. More importantly, this is the first time since 2010 that the two have met in the finals of more than one tournament.
Second-seeded Nishikori of Japan reached the quarterfinals with a 6-3, 4-6 6-3 victory over Argentina's Federico Delbonis.
Roger Federer fought off two match points against Tomas Berdych to make his way into the Miami Open semi-finals and is now expecting a blockbuster match up against Australian bad boy Nick Kyrgios.
Kerber next meets 11th-seeded Venus Williams, who defeated seventh-seeded Svetlana Kuznetsova 6-3, 7-6 (4) in a matchup of former Miami Open champions.
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