The speaker is stuck doing a dull office task, entering and sorting papers, and the afternoon slips away without being noticed. The first line is a long, flat phrase, which suits the monotony it describes. Then the poem turns on the plain admission "I lose the afternoon." Nothing dramatic happens, but there's a quiet sense of waste, as if time has been taken from the speaker rather than spent.
The last two lines shift the mood. The sun is "over," meaning both past its highest point and finished for the day, and it sits above "the under day." That odd phrase suggests the real day, the one of light and air, is going on above while the speaker is beneath it, buried in work. The word "over" in the title does similar double duty, pointing to the sun overhead and to time being up. The feeling is wistful and a little resigned, a small ache about missing the daylight, told in very few words.