"It was a very long match," said Spaniard Ferrer of an epic contest that ran for two hours and 45 minutes before British number one Murray collected his second Masters title with a 7-1 success in the third set tie-break.
He was last world number two in August 2009 when Roger Federer was number one and Rafael Nadal was blighted by injury.
This time only Novak Djokovic is ahead of the Scot with Federer dropping to number three. Ferrer would have gone number four with victory over Murray, but remains ranked fifth behind fourth-placed Nadal.
"I'm sorry I couldn't win it for my supporters," added Ferrer, who had the majority of the crowd behind him but remains without a victory over a top four opponent in any final on the ATP tour. "I am having a very good season. I just needed one point."
Murray was in agreement after collecting his ninth Masters title on tour.
The match hinged on Ferrer's championship point in the 12th game of the third set with Murray trying to force the match to the tie-break on a serve he struggled with all day in some searing heat and wind.
Ferrer challenged a Murray shot that hit the baseline rather than continuing the point, but Hawk-Eye replays showed the ball was in. Murray won the next two points before dominating the tie-break to pick up his second trophy in Miami.
"That is the beauty of the challenge system," said Murray. "Some matches that would have been over. It just dropped in. It was such a tough match that could have gone either way.
"Neither of us played our best tennis, but it was good to get there in the end. I will take four days off and start training on the clay before going to Monte Carlo a week on Wednesday. I did a lot of things well this week, but I need to serve better to win matches more comfortably.
"The rest of my game was pretty good throughout the week."
Murray added: "David is one of the best players in the world. He is a great fighter. I'm sure we will have more tough matches in future."
Murray was never really involved in the first set as he fell 5-0 behind before losing it 6-2. The Scot recovered strongly to force a deciding set by pocketing the final two games of a second set that he won 6-4.
The final set was characterised by breaks of serve before Ferrer became the first man to hold, edging 4-3 clear only for Murray to recover and serve for match leading 5-4.
Ferrer - known as The Wall - was hardly finished and looked the stronger figure as Murray failed to see out the match before hobbling around the court grimacing in trailing 6-5.
He looked a spent force, but there was more drama to come as Murray survived the match point before finally breaking Ferrer's resistance. The Spaniard began to cramp a couple of points before his defeat was finalised by Murray's mental strength.
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