A 6-3 6-3 victory on Sunday earned a second successive ATP World Tour Masters 1000 crown for Djokovic, who also won at Indian Wells last week, and fourth triumph in Miami.
Nadal, by contrast, has yet to taste success in the coastal city, with this latest defeat his fourth in the final of the tournament.
The Spaniard picked up the Comeback of the Year gong earlier this week at the Laureus World Sports Awards, having returned from a lengthy injury absence to claim 10 titles in 2013.
However, he was unable to get the better of his nearest rival in the world rankings, who has now emerged victorious in 14 of their 21 meetings on hard courts.
Remarkably, Djokovic and Nadal now hold all nine Masters 1000 titles between them, with Djokovic having won the last four events at that level as well as the ATP World Tour finals in November 2013.
Both men came into the final well rested after progressing from the last four with walkover victories.
A solitary break of serve was enough to give Djokovic the first set, with the key moment coming in game six.
Nadal, who had a break-point opportunity of his own in the opening game, sent a backhand long at 15-40 to hand his opponent the initiative.
The Serb ruthlessly saw out the first set, winning each of his subsequent service games to 15, and a wonderful cross-court backhand then gave Djokovic another break at the start of set two.
A typically determined Nadal refused to dig in and battled back from 30-40 down to hold serve in the fifth game of the set.
It mattered little, however, as the clinical Djokovic displayed dominant form on his own serve before breaking again to complete an impressive win in one hour and 24 minutes.