The Owls swatted aside Shrewsbury Town but the result was rendered irrelevant after wins for both Plymouth Argyle and Ipswich Town.
The pair both sealed the victories they needed to confirm their places in the Championship next term.
Wednesday will now have to navigate the end-of-season lottery that is the play-offs if they are to join them.
Moore, who watched striker Michael Smith score a hat-trick in the taming of the Shrews, admitted: “There’s always regrets that you can’t go one better.
“But this is football, sometimes when you feel you should get the rub of the green, you haven’t. But what we have got is another wonderful oppportunity and that’s what we have got to be looking at.
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