The Trek-Segafredo rider took the victory in poor conditions as the rain came down intermittently throughout the stage, with the slippery conditions claiming star British time-triallist Alex Dowsett in a crash.
"It was not fun to be standing on the start ramp and seeing the rain," said Cancellara. "You know that it will be wet roads, and I knew then it would be like a poker game. Honestly, I was really nervous for today, and for me, it was really important to win. For many reasons: it's a home race, my last time here, the history…"
Earlier in the day, it had been Reto Hollenstein (IAM) who set the quickest time, but he was soon overhauled once the big hitters were out on the course.
Setting a fast pace in the first half of the prologue was Australian Luke Durbridge (Orica-GreenEDGE) who hit out hard at the start to post the fastest time at the intermediate check of the day and finishing just outside the time of Jurgen Roelandts (Lotto-Soudal) at the finish.
"It was a very pleasing ride for me today," said Durbridge. "I've done some work after the classics on my time trial position and also my time trial training, so I was very happy it's all heading in the right direction now and getting back up there in a big prologue like the Tour de Suisse."
"It's a big confidence booster, so I am really pleased with how it went and to start the tour of this way.
"I was talking to Sam Bewley before I started and he said you can't really make up a lot of time in the back end, so I went full gas at the start and just tried to hold on as much as I could, it was really helpful advice."
Fabian Cancellara followed a different pacing strategy, going through the first time check eight seconds down on Durbridge, but recovering the time in the final kilometres and sprinting to the line to claim the win by a mere six hundredths of a second over second-placed Jurgen Roelandts.
Before the start Cancellara had team mechanics on standby to do some wheel changes dependent on the conditions and he was clearly very invested in taking the win in his swansong appearance at the Swiss race.
"I had wheels ready at the start for wet and dry and in the end I took the tires for the dry because super slick goes better. But then I had wet roads on some of the corners, and it was hard to maintain the rhythm, the speed. I had rain from the climb to the chicane – around two kilometers, and the downhill was wet."
"In the end, I did what I could, and it worked out. Having a win in my last Tour de Suisse means a lot, this stands out. I will enjoy the night and the day tomorrow in the yellow. I will do what I can to try and defend, but it's going to be a hard week, but we go on in yellow tomorrow, and that is what is nice."
The first road stage of the Tour de Suisse is around a hilly circuit near Baar but will still likely be a stage for the sprinters like Peter Sagan (Tinkoff), Michael Matthews (Orica-GreenEDGE) and Fernando Gaviria (Etixx-QuickStep).