The top seed for the tournament was ousted 6-4, 0-6, 6-4 by the Russian teenager, who also knocked her out of the Apia International in Sydney in January.
"I was not feeling the best today - I'm trying to find my rhythm," the 29-year-old said in her post-match press conference.
"But she [Kasatkina] plays good. I make too many mistakes in the important moments. I think it was, for sure, not my day."
? WTA (@WTA) February 16, 2017
Kerber was let down by a proliferation of unforced errors in her 4-6, 6-0, 4-6 loss, but refused to blame it on the Doha rain delays affecting her concentration.
"Of course, the weather, it can happen like this," she said. "I think this is not a big deal. Of course, we have to wait a lot, but yeah, this is not a big deal, I think, for us players."
The German now turns her attention to the Dubai Duty Free Tennis Championships, which begins on February 19.
"First of all, I have to get ready again and feeling good because, yeah, I was not feeling very good in the last few days," she admitted. "I think this is the most important thing for me right now. Then, of course, looking forward to the next week [in Dubai]."