The Australian contested the 6.7km time trial course early in the proceedings, with his fast time of 7min 40sec putting him in the hot seat.
In the end it was only Kwiatkowski, the road race world champion, who could beat Dennis's time, finishing less than one second ahead of the BMC rider.
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Kwiatkowski's Etixx-QuickStep team-mate Tony Martin finished third, seven seconds behind, while many of the favourites finished outside of the top 10.
Sky just managed to crack the top 10, with Geraint Thomas in 10th, 14 seconds back. Time trial world champion Bradley Wiggins was 12th and former Paris-Nice winner Richie Porte 13th, both 12 seconds in arrears.
Dennis's BMC team-mate Tejay van Garderen finished 11th.
Orica-GreenEDGE's Michael Matthews put in a strong performance in his first race this season to finish eighth, 12 seconds back.
Kwiatkowski has a one second lead to defend in the 196.5km Stage 1 from Saint-Remy-Les-Chevreuse to Contres.
Prologue and General Classification
1 Michal Kwiatkowski (POL) Etixx-QuickStep 7min 40sec
2 Rohan Dennis (AUS) BMC
3 Tony Martin (GER) Etixx-QuickStep 0:00:07
4 Luis Leon Sanchez (ESP) Astana 0:00:10
5 Lars Boom (NED) Astana
6 John Degenkolb (GER) Giant-Alpecin
7 Sylvain Chavanel (FRA) IAM
8 Michael Matthews (AUS) Orica-GreenEDGE 0:00:12
9 Tom Dumoulin (NED) Giant-Alpecin 0:00:13
10 Geraint Thomas (GBR) Sky 0:00:14