The 38-year-old Paes, who will be going for his sixth Olympics in London later this year, thus won his third straight title in Miami, having triumphed with Lukas Dlouhy in 2010 and Mahesh Bhupathi in 2011, also became the 24th player to accomplish 50 doubles titles on the ATP World Tour.
With thunder rolling off suspected tornado clouds in the Miami area and a 10-minute pause in the second set as rain drops fell, the match didn't lack for drama. The lights had to be turned on at mid-afternoon for play to continue.
The victory in 82 minutes gave the newly formed Paes-Stepanek team, the Australian Open champions, another victory over Nestor's side after a win in the Melbourne semifinals.
Nestor and Mirnyi failed to add to their total of two titles this season, obtained in Brisbane at the start of the year and Memphis in February.
“This was a tough loss, but there's a lot of tennis to play this year,” said the 39-year-old from Toronto. “We had our chances but they were just too good in the tiebreak set.
“They really got on top of us after we lead and then ran away with it,” said Nestor, who won the Miami title a decade ago with former partner Mark Knowles of the Bahamas.
Nestor and his partner played a solid opening set, with the second seeds getting a break for 3-1 as the experienced Paes double-faulted.
The Canadian's team took advantage of the opportunity, with Nestor firing a cross-court winner for 4-1 and serving out the seventh game with an ace to lead 5-2.
The set ended a game later with another break, with Nestor executing a graceful backhand overhead on the first of three set points to seal the lead after 33 minutes.
The tables turned in the second set as the threatening weather moved in. A pair of breaks gave the Paes-led team a 4-0 lead after Nestor went down on serve after saving three break points.
With the teams sitting under umbrellas due to the weather as Nestor-Mirnyi trailed 5-0, the momentum continued to shift. Paes and Stepanek claimed the set on a volley winner and took the match into the deciding tie-break set.
Nestor's side earned a 4-1 lead only to watch their opponents run off six straight points for a 7-4 margin. After missing on two match points, Paes produced another untouchable volley to lift the title.
The newly-formed Indo-Czech pair, the Australian Open champions, had beaten Nestor-Mirnyi side in the semi-finals of the Melbourne event too.
Having beaten the Bryan twins, Bob and Mike, in the previous round, Paes and Stepanek were on a high, but failed to get the early momentum going.
However, once they settled down after being broken twice in the first set, there was little Nestor and Mirnyi could do to contain them.