Former world champion Gilbert beat Germany's Nils Politt in a sprint finish to win the 257km race in five hours 58 minutes two seconds.
Gilbert's compatriot and Deceuninck-Quick-Step team-mate Yves Lampaert finished third.
The five monuments are cycling's most prestigious one-day races - Gilbert has won them all except the Milan-San Remo.
"I still have this dream to win all of them. Little by little I'm getting there," Gilbert said.
The 36-year-old made his first move with 70km remaining and easily outsprinted his closest rival Politt to ensure victory.
"Politt's very courageous. In the end the best rider won, and thankfully it was me," Gilbert added.
"I've always wanted to win all the monuments, and I'm getting closer now."
Only three riders have won all five monuments - Belgian riders Rik van Looy, Eddy Merckx and Roger de Vlaeminck.
Paris-Roubaix results
1. Philippe Gilbert (Bel/Deceuninck-Quick Step) 5hrs 58mins 02secs
2. Nils Politt (Ger/Katusha-Alpecin) Same time
3. Yves Lampaert (Bel/Deceuninck-Quick Step) + 13secs
4. Sep Vanmarcke (Bel/EF Education First) +40secs
5. Peter Sagan (Svk/Bora-Hansgrohe) +42secs