"I wasn't at my best. I really felt the effects of the antibiotics, and I still felt it in the lungs, for sure. I really raced on mental strength," Naesen told reporters at the finish in Oudenaarde, Belgium.
"On paper, it was my best result at Flanders, but I would already have been on the podium if I hadn't have crashed on the Kwaremont in 2017. On paper it's my best result, but it wasn't my best race," he said.
A healthy Naesen may well have been in better contention for the Ronde title, but he was nevertheless among the favourites in the group that was led home by 2015 winner Alexander Kristoff (UAE Team Emirates), with none of Peter Sagan (Bora-Hansgrohe), Mathieu van der Poel (Correndon-Circus), Wout van Aert (Jumbo-Visma) or Naesen's training partner Greg Van Avermaet (CCC Team) able to catch race winner Alberto Bettiol (EF Education First), who slipped away on the final climb of the Kwaremont.
"He was very strong," Naesen said of Bettiol's ride. "He was really very, very strong. We didn't collaborate much on the run-in [to the finish], but on the Kwaremont and Paterberg, I felt as though we were going very, very fast.
"They're climbs that suit me very well, and I know them by heart, as I often do them in training. They were good for me, but, if I'm at my best, I do them quicker than that," he said.
At one stage, it looked as though Naesen may miss out on fighting it out for the win not because of illness, but because he got a puncture just before the start of the climb of the Kruisberg with just under 30km to go.
"That hurt," he admitted. "It started to split on the Kruisberg – and I knew that it was going to. But I got back up there quickly, and that was thanks to experience.
"Honestly, I'm satisfied with this position," Naesen added. "It's not a result I dream about, but with the armoury I had today, it's not bad."
As he recovers from sickness, Naesen can look forward to giving it another go at next weekend's Paris-Roubaix, where he'll again hope to be in contention on the cobbles.
"Tomorrow [Monday] I can stop the antibiotics," he said, "and I hope to feel better and be able to have more of an impact on the race."