Best, whose brother Simon also captained Ireland, previously took on the captaincy duties for Ireland in their summer tour wins over Canada and the USA in 2009.
"It's a great honour to captain your country. It's something growing up that you dream of doing," said the Ulster hooker.
"It's very unfortunate what has happened to Paulie, but I was obviously very honoured when Declan (Kidney) asked me to captain the side.
"We know we'll have to be on the money against Scotland. It will be a massive challenge for our defence."
Donncha Ryan will start his first RBS 6 Nations game in the second row, having featured as a replacement in five previous games in the Championship.
Connacht's versatile forward Mike McCarthy, who made his Ireland debut in the GUINNESS Summer Series last August, has been promoted to the replacements bench.
Meanwhile, Eoin Reddan will partner Jonathan Sexton at scrum half in place of the injured Conor Murray with Tomas O'Leary added to the bench.
IRELAND Team & Replacements (v Scotland, 2012 RBS 6 Nations Championship, Aviva Stadium, Saturday, March 10, kick-off 5pm):
15 - Rob Kearney (UCD/Leinster)
14 - Tommy Bowe (Ospreys)
13 - Keith Earls (Young Munster/Munster)
12 - Gordon D'Arcy (Lansdowne/Leinster)
10 - Jonathan Sexton (St. Mary's College/Leinster)
9 - Eoin Reddan (Lansdowne/Leinster)
1 - Cian Healy (Clontarf/Leinster)
2 - Rory Best (Banbridge/Ulster) (capt)
3 - Mike Ross (Clontarf/Leinster)
4 - Donncha O'Callaghan (Cork Constitution/Munster)
5 - Donnacha Ryan (Shannon/Munster)
6 - Stephen Ferris (Dungannon/Ulster)
7 - Sean O'Brien (Clontarf/Leinster)
8 - Jamie Heaslip (Naas/Leinster)
16 - Sean Cronin (St. Mary's College/Leinster)
17 - Tom Court (Malone/Ulster)
18 - Mike McCarthy (Buccaneers/Connacht)
19 - Peter O'Mahony (Cork Constitution/Munster)
20 - Tomas O'Leary (Dolphin/Munster)
21 - Ronan O'Gara (Cork Constitution/Munster)
22 - Fergus McFadden (Old Belvedere/Leinster)