Boonen hit the deck with some 65 kilometres left and looked to be in some pain. He got back on his bike but a few minutes later quit the race which was won in impressive fashion by Slovak Peter Sagan.
Boonen had hoped to retain his Gent-Wevelgem, Tour of Flanders and Paris-Roubaix titles but his early season has been disrupted after surgery on an infected elbow in January.
Another Tour of Flanders favourite, Swiss Fabian Cancellara, quit at the feed zone, possibly to stay fresh for next weekend.
Sagan, who finished second in Milan-San Remo and the GP E3, attacked a group of breakaway riders with four kilometres left and was never caught.
The race was slashed by 45 km because of snow in the vicinity of Gent.