The Frenchman was well up on Dumoulin’s best time at the halfway timing point and was able to hold on to his advantage over the second half of the hilly route.
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Chris Froome (Team Sky) led the stage for a few minutes earlier in the day, setting off early after losing 17 minutes on Thursday’s stage two, but his mark was beaten by Bob Jungels (Etixx-Quick Step) by less than a second.
Race leader Nairo Quintana (Movistar) put in a strong performance to clock the same time as Froome and hold on to his overall lead, with Pinot moving up to second in the classification.
Saturday’s stage four will see Quintana defending his lead, with three category one climbs, including the summit finish at Villars-sur-Ollon.
Tour de Romandie stage three, Sion – Sion (15.1km ITT)
1. Thibaut Pinot (Fra) FDJ, 20-21
2. Tom Dumoulin (Ned) Giant-Alpecin, at 2s
3. Bob Jungels (Lux) Etixx-Quick Step, at 9s
4. Chris Froome (GBr) Team Sky, st
5. Jerome Coppel (Fra) IAM Cycling, st
6. Nairo Quintana (Col) Movistar, st
7. Ilnur Zakarin (Rus) Katusha, at 17s
8. Ion Izagirre (Esp) Movistar, at 18s
9. Steve Morabito (Swi) FDJ, at 22s
10. Manuele Boaro (Ita) Tinkoff, at 25s
Overall standings after stage three
1. Nairo Quintana (Col) Movistar, 7-22-35
2. Thibaut Pinot (Fra) FDJ, at 23s
3. Ilnur Zakarin (Rus) Katusha, at 26s
4. Ion Izagirre (Esp) Movistar, at 29s
5. Tom Dumoulin (Ned) Giant-Alpecin, at 50s
6. Matthias Frank (Swi) IAM Cycling, at 1-06
7. Simon Spilak (Slo) Katusha, at 1-11
8. Rui Costa (Por) Lampre-Merida, at 1-12
9. Tejay van Garderen (USA) BMC, at 1-22
10. Rafal Majka (Pol) Tinkoff, at 1-23