Boonen fell in the final kilometre as the teams revved up their engines for the final blast.
Early reports suggest that he touched his front wheel with another rider's rear wheel. He crossed the line with the back of his jersey ripped in several spots and rode to the 25km to the hotel.
"It was on the other side of the road from where I was," Kristoff explained of the crash.
"I heard on the right side there was a crash and heard later it was Tom, which was a pity. For sure he'll try again another day if he's not badly injured."
The Norwegian, who already one once this year in the Etoile de Bessèges, finished ahead of Italians Kristian Sbaragli (Dimension Data) and Sonny Colbrelli (Bahrain-Merida).
Marco Haller kept him out of danger in the final kilometre after Katusha worked earlier in the day.
"I knew it'd be a headwind and very tight with a lot of riders because they sit on the wheel and then they come to the front. I made sure I was on the left side where it was more open," Kristoff added.
Boonen's team "Quick-Step took the right side and waited, and it was really tight. They were unlucky. I think Boonen went down with one kilometre to go.
"He would have made for tough competition in the end, so that was a pity. With the chaos, I'm happy I was able to come to the front without crashing."
Quick Step's sports directors arrived and parked in the adjacent garden. They said that they would not comment because they had not seen the crash, but later confirmed that Boonen would start stage two on Wednesday.
The crash and Kristoff's sprint sparked the tail-end of a quiet day through the rugged Oman countryside dotted occasionally with Simr trees.
"It's always nice to start with wins. We already managed to get one in Oman on the first day," Kristoff said.
"If we get any more it'll be a bonus and it'll be great. The last stage will be for me, but we have riders for the other stages. We are going to be doing some good training here in Oman and getting ourselves ready for the races to come."
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