Greg van Avermaet (BMC) outsprinted Gilbert's team-mate Niki Terpstra to the second step on the podium.
Peter Sagan's (Bora-Hansgrohe) chances came crashing down with his fall on the Oude Kwaremont with 17km to go. Van Avermaet too was caught up in the crash but remounted quickly enough for his podium place.
A mechanical with just 37km left in Boonen's Ronde career derailed any scrap of a fairy tale ending that may have remained with his team-mate Gilbert up the road.
Boonen looked in vintage form. Although many said before the race the Muur would not prove decisive at 90km to go, he drove the pace hard and a split of around 15 riders evolved. The group caught the remains of the day's eight-rider break with 70km to go.
After the race, Gilbert clarified how the race unfolded in his and not Boonen's favour.
“We won as a team today and everyone deserves to be on the podium, so a big thanks goes to all the guys, because they did a huge workload," Gilbert said.
"After Tom initiated that move on the Muur, we continued to push and decided to go full gas on the second ascent of the Oude Kwaremont. Tom did a big pull just ahead of the hill, I took over as the road began to rise and soon noticed I opened a small gap and never looked back again.
"Many people thought I was crazy to attack 55 kilometers out, myself included, but I didn’t go that hard, because I was aware the final 15 kilometers were very tough, so I kept some energy which I knew would prove very useful for that last part of the race”, said Philippe Gilbert, only the second Wallon rider in history to triumph at De Ronde.
“When I approached the final kilometer, I looked behind and saw the chasers were still a long way back and thought of a nice way of celebrating my success. That’s why I raised my bike over my head because it was an important part of my victory. I’m really proud of how I managed today’s race and of what I achieved!”
Both Sagan and Van Avermaet missed this move and played catch-up the rest of the day, but through general attrition and effort, their position ultimately improved to form the second group out on the road behind Gilbert.
While it will be argued aplenty by cycling pundits whether Sagan and Van Avermaet could've caught Gilbert if it were not for their tangle, at which point they were 59 seconds in arrears, one thing did seem clear, Sagan may have made a bad decision riding too close to the barriers.