How can I justify having only two publications when applying for postdoc jobs in physics/chemistry? I have only 2 publications from my PhD, and I am applying for a post-doc position. 

My fields are: Theoretical physical chemistry; condensed matter physics; 
computational chemistry; cluster science.

I am already a postdoc and I am finishing 2 publications, and my collaborators are going to write other 2. The problems are: I have no idea when those 2 papers, that I am going to be co-author, will be published; the only proof I have publications is those 2 from my PhD, which are not really connected with the position I am applying for.

How to justify the lack of publications in my application form?
I always had this feeling that putting "manuscript in preparation" in my publication list sounds weird, even if it is true.
I do not understand why you find "weird" putting manuscripts in preparation in your CV. In my field, it is perfectly normal and accepted, and I guess in all academia.

This is the best way to explain what you did in the last years. It won't be strange at all, especially if you have talks on those results already, as you imply in a comment. These things happen; sometimes papers take a long time to prepare, and a selection committee should be aware of this fact.

It would look much weirder, in my view, if you don't list them and write a long statement in the cover letter about the lack of publications. As they said in ancient Rome, "he who excuses himself unsolicited, accuses himself".