The Swiss rider held-off Jarlinson Pantano (IAM Cycling) and Julian Alaphilippe (Etixx-Quick-Step) at the stage finish in Saint-Imier, with Australia's Nathan Haas (Cannondale-Garmin) in fourth. A group of 50 riders contested the finish after cresting the final climb together.
“I actually was hurting a lot on the second last climb out here in Saint-Imier,” said Albasini who won three stages in last year's race.
“But (the final climb) was quite a regular climb. After a really fast first part, the second part was more regular and I could stay in the bunch so I knew I had a good chance in the sprint.”
“I placed myself well, I always like a little fight going on and I was maybe a little bit too far in the front too early so I was happy the guys from Garmin came around me and I could jump on them.
“Still I had to do a long long sprint so I was happy to keep (the lead).”
The victory is consolation for Orica-GreenEDGE after the team finished second to Sky in the opening team time trial by less than one second.
“It was disappointing yesterday so I am super happy that we can have the first win today,” Albasini said. “It makes it a little bit better for the 0.63 of a second we lost yesterday.”
Overnight leader Geraint Thomas (Sky) suffered a puncture with 22 kilometres to go, at the base of the Vue des Alpes. Despite assistance from team-mate Peter Kennaugh he was never able to rejoin the front of the race, eventually finishing over four minutes down.
Attacks on the final climb - including ones by Romain Bardet (Ag2r-La Mondiale) and Rafal Majka (Tinkoff-Saxo) - failed to force a selection at the front of the race. Astana’s Rein Taaramae eventually managed to forge a slim lead, but a huge effort by Tony Martin (Etixx-Quick-Step) ensured he was caught with two kilometres to go to set up a sprint finish.
Albasini holds a 10 second lead over Chris Froome (Sky) with his team-mates Ivan Santaromita and Simon Yates also on the same time.
Stage 2: 168.1km, Apples - Saint-Imier
1 Michael Albasini (SWI) Orica-GreenEDGE 4hr 21min 43sec
2 Jarlinson Pantano (COL) IAM Cycling
3 Julian Alaphilippe (FRA) Etixx-Quick-Step
4 Nathan Haas (AUS) Cannondale-Garmin
5 Rui Costa (POR) Lampre-Merida
6 Damiano Caruso (ITA) BMC Racing
7 Ilnur Zakarin (RUS) Katusha
8 Ivan Santaromita (ITA) Orica-GreenEDGE
9 Jan Bakelants (BEL) AG2R La Mondiale
10 Ramunas Navardauskas (LTU) Cannondale-Garmin
General Classification
1 Michael Albasini (SWI) Orica-GreenEDGE 4hr 42min 52sec
2 Ivan Santaromita (ITA) Orica-GreenEDGE 0:00:10
3 Christopher Froome (GBR) Sky
4 Simon Yates (GBR) Orica-GreenEDGE
5 Ilnur Zakarin (RUS) Katusha 0:00:15
6 Pavel Kochetkov (RUS) Katusha
7 Egor Silin (RUS) Katusha
8 Yury Trofimov (RUS) Katusha
9 Simon Spilak (SLO) Katusha
10 Julian Alaphilippe (FRA) Etixx-Quick-Step 0:00:20
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