Do I need to fill a separate DS-160 application for her?
If yes, how do I do that without a passport or travel document?
You cannot. To travel to the United States with your daughter, you will need to get her a passport.
The US still has a regulation on the books that permits issuing visas when more than one person is listed in a single passport (22 CFR 41.104(c)):
(c) A single passport including more than one person
The passport requirement for a nonimmigrant visa may be met by the presentation of a passport including more than one person, if such inclusion is authorized under the laws or regulations of the issuing authority and if a photograph of each visa applicant 16 years of age or over has been attached to the passport by the issuing authority.
I suspect that this may be obsolete, but it seems that it doesn't matter in your case because Pakistan apparently does not list children in parents' passports (indeed, the practice has been abandoned by most countries as far as I know). I did not find an official source for this information, but I also did not see any evidence to the contrary in the official sources that I did find. The unofficial source, which links to a couple of government sites, is https://pakguide.pk/apply-for-new-passport/. It says, as the third bullet point under "important notes":
Children are issued their separate passport