Kittel, of the Quick Step Floors team, ended up with a bloodied face after sustaining a cut to his eyebrow, failing to contest the final sprint after winning the first two stages of the race, which he still leads.
Kittel left with blood pouring from face after alleged punch
"I got punched by Andriy Grivko from Astana. That's why I had blood on my face but I didn't crash," Kittel said in a statement.
Grivko handed 45-day ban over Dubai Tour bust-up with Kittel
"There was some confusion in the race. My team worked well for the sprint but I was not in a perfect position and maybe my head was elsewhere too."
Astana apologised to Kittel and his team, saying on Twitter: "Astana Proteam apologizes to @marcelkittel and @quickstepteam for improper behavior of its rider @andrei_007 during stage 3 of @dubaitour".
The Tour of Dubai ends on Saturday.