The Polish national TT champion was the 107th rider down the ramp out of 153 starters, but covered the short course the fastest, with a time of seven minutes and 25 seconds.
Kwiatkowski narrowly beat the time of Jos van Emden (LottoNL-Jumbo) by just one second, set over an hour before.
"After 40 days without racing it was a bit of a surprise," he said. "But I know how hard I was training to be in good shape for the Dauphiné as well as preparing for the Tour so you have to always be on the start thinking about the win otherwise you aren't able to perform well.
Kwiatkowski's teammate Geraint Thomas crashed on a right-hand corner halfway through his run and saw him cross the line 21 seconds off the pace. It also prompted a question as to the leadership of the team at the race.
"Both of us, Geraint and myself," Kwiatkowski replied. "We came here to see how the shape is going before the Tour. I have the advantage winning the prologue but there's harder stages by the end of the race, four mountain finishes and the team time trial so for sure we are looking forward to race hard.
"It was a really fast bend you have to be really careful there. I hope he's alright because I know G can fight for the win, I hope he's alright that it's nothing serious.
"I just want to enjoy my victory. I had my birthday yesterday. It might be my last time in the national TT jersey."
Bob Jungels (Quick-Step Floors) who could race strongly here, impressed with his effort just seven seconds off Kwiatkowski's. Movistar's leader Marc Soler is the best placed of the other main GC contenders, finishing his TT 20 seconds down. Mitchelton-Scott's hope Adam Yates is also there and thereabouts at 21 seconds, as are Romain Bardet (Ag2R) and Vincenzo Nibali (Bahrain Merida) who finished the day 23 and 24 seconds off the pace respectively.
National road race champion Alex Edmondson was the fastest Aussie, finishing just outside the top 10 with his time of seven minutes and 36 seconds.
The race continues with a punchy 179km first stage from Valence to Saint-Just-Saint-Rambert which is scattered with low category climbs. It will be streamed here and broadcast on SBS Viceland from 11:15pm AEST.
Stage 1: 179km from Valence to Saint-Just-Saint-Rambert. Source: Supplied
