Britain’s Ben Swift led the peloton – which swallowed up the lead group late on – to finish second with Michal Kwiatkowski finishing third for the second day in a row.
Stage one victor Alberto Contador rebuffed a series of late attacks from Alejandro Valverde to stay atop the general classification.
The early break consisting of Martin, fellow QuickStep rider Jan Bakelants, Bob Jungels, Maxime Monfort, Hubert Dupont, Gorka Izagirre and David Malacarne amassed a sizable advantage during the early hilly stages as the race journeyed from Ordizia to Dantxarinea.
The undulating terrain eventually took its toll and, with the lead lingering around the minute mark, Martin attacked from 20 kilometres out.
The German’s acceleration destroyed the breakaway group with only Bakelants and Izagirre able to respond.
Bakelants' final act was a short burst to propel his team-mate clear, and Martin obliged to power through the closing kilometres to claim a dominant win by 30 seconds.
Stage two results
1. Tony Martin (Germany / Omega Pharma - Quick-Step) 3:46:17"
2. Ben Swift (Britain / Team Sky) +30"
3. Michal Kwiatkowski (Poland / Omega Pharma - Quick-Step)
4. Damiano Cunego (Italy / Lampre)
5. Paul Martens (Germany / Belkin)
6. Alejandro Valverde (Spain / Movistar)
7. Maxim Iglinskiy (Kazakhstan / Astana)
8. Yukiya Arashiro (Japan / Europcar)
9. Michael Matthews (Australia / Orica)
10. Rinaldo Nocentini (Italy / AG2R)
1. Alberto Contador (Spain / Tinkoff - Saxo) 7:51:54"
2. Alejandro Valverde (Spain / Movistar) +14"
3. Michal Kwiatkowski (Poland / Omega Pharma - Quick-Step) +34"
4. Damiano Cunego (Italy / Lampre) +36"
5. Cadel Evans (Australia / BMC Racing)
6. Jean-Christophe Peraud (France / AG2R)
7. Mikel Nieve (Spain / Team Sky)
8. Yury Trofimov (Russia / Katusha)
9. Roman Kreuziger (Czech Republic / Tinkoff - Saxo) +54"
10. Mikel Landa (Spain / Astana)
- Sports & Recreation
- Michal Kwiatkowski
- Alejandro Valverde
- Alberto Contador
- Tony Martin
- Gorka Izagirre
- Omega Pharma