Some time after his return from the death, Clark realises Bruce Wayne is Batman (let's assume he didn't already find out in the movie). Maybe he runs into Bruce again at some gala and suddenly recognises his mouth, his eyes, his smell, his heart beat, the fractures on his bones. He feels like he should tell Bruce he knows, but he also feels kinda guilty about knowing, like he snooped and invaded Bruce's privacy. So he doesn't say anything, but he still approaches Bruce because it blows his mind that this cynical, smarmy rich asshole is Batman, the badass he's been working with for a while now. And sooner or later, Clark and Bruce Wayne end up in bed together and Clark still feels guilty for not telling him he knows who he is.

I'd assume that Bruce knows who Clark is, but Clark has no idea Bruce knows, but Bruce being oblivious to Clark's secret identity works, too.