Boonen finished second under a scorching sun in Al Wutayyah, narrowly behind Astana’s Andrea Guardini.
Four-time Paris-Roubaix winner Boonen had to start his sprint earlier than planned after team-mate Matteo Trentin dropped him off 250 metres from the line, but couldn’t quite hold off Guardini on the uphill drag.
“I gave a good sprint but the finish line was 50 metres too long,” he said. “If it was 50 metres shorter, I may have won.
“We had done good work in the last five kilometres for the sprint, but in the 300 metres, I had to go, because I had everyone in the wheel.
“I was like a locomotive for them, and the line was still too far away, with a headwind and two to three per cent slope.”
Nonetheless, the 34-year-old was pleased that his preparation for the Classics took another step forward.
“In Oman, we do not need to come here as the favorites, and do the work every day like in Qatar,” he said. “But I want to try my luck a few times in the sprints and today it was an opportunity, especially as the stage was not difficult.
“I’m disappointed [with the result] because we did a lot of work in the final kilometres, but my feelings are really good.”