Joined by Team Sky teammate Michal Golas, the pair spent almost the entire 204-kilometre race up the road as part of a select breakaway.
After tireless work from Golas as the laps ticked off, Kwiatkowski was able to narrowly out-sprint Maciej Bodnar (Bora-Hansgrohe) at the line to claim a second elite road title.
Golas had a perfect view of the sprint as he finished fourth, while Lukasz Wisniowski was able to sit in the chasing pack behind, giving the team another card to play on a day of great teamwork.
Mirroring his success of 2013, Kwiatkowski will don his national colours across the next 12 months of racing.
Elsewhere on Sunday Jonathan Castroviejo was back in action following his Spanish time trial victory. The Team Sky rider finished 19th in Benicassim, in a race won by Gorka Izagirre (Bahrain Merida). Kristoffer Halvorsen was also in action in Norway, as a breakaway held on to claim victory.
After the race a happy Kwiatkowski said: "I'm more than happy to win my second Polish road race title. This was without a doubt one of the toughest races of my life. 200 kilometres in the breakaway, with Polish teams chasing very hard.
"We did everything according to the plan and attacked in the first crosswinds. I owe everything to Goły - he is the true hero of this race and the engine of the breakaway, pulling so hard for countless kilometres.
"It will be a fantastic feeling to wear Polish Champion jersey in the biggest races."