Murray was beaten 7-6 4-6 6-0 in Sunday’s title decider but his run to the final was enough for him to climb above Rafael Nadal into third spot on the new ATP list.
Kei Nishikori also moves above Nadal, who slips to fifth following his last-32 loss to Fernando Verdasco in Miami.
Nadal is now less than 200 points ahead of sixth-placed Milos Raonic. The last time the Spaniard was ranked outside the top five was in May 2005 – before he had won any of his 14 Grand Slam titles.
Djokovic now holds a lead of more than 4,000 points over Roger Federer at the top of the rankings. The winner of Grand Slam claims 2,000 points, while 1,000 are awarded to champions of the Masters tournaments, of which Miami is one.
This week is his 141st on top of the pile, equalling the number of weeks Nadal has spent in top spot. Only Roger Federer (302), Pete Sampras (286), Ivan Lendl (270), Jimmy Connors (268) and John McEnroe (170) have accumulated more weeks as world number one.
Further down the list, new British recruit Aljaz Bedene drops to 99th. The Slovenian-born player officially changed his nationality last week having lived in Britain for several years.
In the WTA rankings, Serena Williams maintains her hold on top spot after winning in Miami.
British number one Heather Watson stays in 41st, three places below her career-high, following a second-round loss to Angelique Kerber in Florida.