In threatening spring form, Kwiatkowski finally claimed his first Sky win, timing the sprint perfectly with 200m to go, with Sagan left behind to again ask questions.
Sky team-mate Ian Stannard rounded out the podium, topping off a successful day for the team after Poels' Stage 5 win at the Volta a Catalunya.
The dynamic Kwiatkowski and 2014 winner, Sagan attacked the main group with 31km to go, collaborating well to gain as much as a 36-second lead.
An early break formed with eight riders gaining a maximum lead of six minutes which dropped immediately once Trek-Segafredo drove the peloton hard to the Taaienberg with 74kms to go.
A significant split finally formed in the 206.4km cobbled Flemish classic when a large group of favorites attacked on the Taaienberg. Containing the likes of Jurgen Roelandts (Lotto-Soudal), Fabian Cancellara (Trek-Segafredo), and Tom Boonen (Etixx-Quickstep) the move looked dangerous even with around 70 kilometres remaining.
Cancellara however suffered a mechanical at the bottom of the Boigneberg and waited over a minute for assistance. An extraordinary effort by his team-mates brought him back to the group before Sagan and Kwiatowski launched their bold move on the Karnemelkbeekstraat.
"I was really motivated today and I did my best. I was perfectly protected by my team-mates, Ian Stannard was always there for me and then me and Peter worked together well," Kwiatkowski said.
"Me and Peter did a really good race. I knew I had to go with a long sprint because his kick is bigger than mine, and that worked out. I didn't look back and went full gas to the finish."