I think that it's simply a matter of that, once Holly has seen Lime, and Calloway and Sgt. Paine realize that Lime disappeared into the sewer, finally everything makes sense and they know he's still alive, was "the third man," thus that the buried dead body surely is the missing hospital orderly Harbin.

Holly and Calloway had earlier gotten more or less on the same page, and established trust, with one another when Calloway explained about the penicillin.