Cancellara took his second victory of 2016, defeating Martin by just five seconds and Geraint Thomas (Sky) by 28 seconds, on the flat 18km time-trial course. While he felt confident, Cancellara confessed the win wasn't easy.
"The race was one-quarter technical in the first part and three-quarters with more power straights. A lot of wind, tail-wind and cross-wind; it was a really tough one," he said.
"After yesterday's hard stage I did not have a huge crazy expectation of going for the win. I knew I started early, and Martin and Thomas so late. So I just focused on myself, on my performance. I did my usual warm-up, and I had good feelings. I knew it was going to be a 21-minute race, and I just gave it all knowing what the effort would be.
"And then it was waiting, waiting on the hotseat. I am kind of surprised, but on the other hand super happy about the win," he said.
In the final 7km, both Martin and Thomas faded. Earlier, Thomas crossed the 11.3km time check with the same time as Cancellara and Martin was eight seconds ahead.
Martin now leads the general classification with a three second advantage over Geraint Thomas and 20 seconds on Ion Izagirre (Movistar). Race leader after Stage 2, Luis Leon Sanchez (Astana) crashed on a roundabout and was forced to withdraw from the race.
The wind also proved too much for Alberto Contador (Tinkoff), although his performance edged him into the top ten on GC.
"It was a very, very windy time-trial and the heavier riders could use spoke front wheels,' he said.
"I opted to go with less depth in order to be focused on the race and not on worrying whether I would crash.
“The first part went quite better because it was more or less uphill and being lighter gives you a slim advantage. However, the heavier riders were able to gain time in the second part, slightly downhill and at a faster pace. That's where they gained time on me," he said.
"We don't have any chances at the GC, so we'll see whether we can aim at a stage win (on Sunday).”
Cancellara looks ahead now to Strade Bianche and Tirreno-Adriatico.
"I don't say that today's win gives me more confidence because the confidence I need is more from races like Tirreno-Adriatico because this will show me that I am in the right way," he said.
"There is still some work to do; next week I will take a small rest and move on again with Strade [Bianche] and Tirreno. I still need more, because I need to compete with the others who have been racing in Qatar and Oman. I am just enjoying riding my bike, riding the races, and this makes me feel relaxed. To take another win on top is super cool for myself and super nice for the team and for the motivation for everyone."