After a strong start from Fulham, Mason Mount slipped a slide-rule pass through for the German striker, who squeezed an effort past Alphonse Areola.
Edouard Mendy made a couple of good stops from Ademola Lookman and Ola Aina, and Areola denied Hakim Ziyech at the other end, all before half-time, but in the second half there was little danger to the Chelsea goal.
The game was put beyond doubt when Havertz drifted in from the right and exchanged passes with Timo Werner before breaking the offside trap and slotting home.
The win puts Chelsea six points clear of West Ham having played a game more, and just two behind Leicester in third, while Fulham are nine points adrift of safety with just four games remaining.
