The Collaborative International Dictionary of English v.0.48:

Confute \Con*fute\, v. t. [imp. & p. p. Confuted; p. pr. & vb.
   n. Confuting.] [L. confutare to chek (a boiling liquid), to
   repress, confute; con- + a root seen in futis a water
   vessel), prob. akin to fundere to pour: cf. F. confuter. See
   Fuse to melt.]
   To overwhelm by argument; to refute conclusively; to prove or
   show to be false or defective; to overcome; to silence.
   [1913 Webster]

         Satan stood . . . confuted and convinced
         Of his weak arguing fallacious drift.    --Milton.
   [1913 Webster]

         No man's error can be confuted who doth not . . . grant
         some true principle that contradicts his error.
                                                  --Chillingworth.
   [1913 Webster]

         I confute a good profession with a bad conversation.
                                                  --Fuller.

   Syn: To disprove; overthrow; sed aside; refute; oppugn.

   Usage: To Confute, Refute. Refute is literally to and
          decisive evidence; as, to refute a calumny, charge,
          etc. Confute is literally to check boiling, as when
          cold water is poured into hot, thus serving to allay,
          bring down, or neutralize completely. Hence, as
          applied to arguments (and the word is never applied,
          like refute, to charges), it denotes, to overwhelm by
          evidence which puts an end to the case and leaves an
          opponent nothing to say; to silence; as, "the atheist
          is confuted by the whole structure of things around
          him."
          [1913 Webster]

WordNet (r) 3.0 (2006):

confute
    v 1: prove to be false; "The physicist disproved his colleagues'
         theories" [syn: disprove, confute] [ant: demonstrate,
         establish, prove, shew, show]

Moby Thesaurus II by Grady Ward, 1.0:

71 Moby Thesaurus words for "confute":
   answer, answer conclusively, antagonize, argue down,
   be antipathetic, be inimical, beat against, break, clash, collide,
   conflict, conflict with, confound, contradict, contrapose,
   contravene, controvert, counter, counteract, counterattack,
   countercharge, counterclaim, counterpose, countervail, counterwork,
   cross, crush, defeat, demolish, deny, disconfirm, dismiss,
   dispose of, evert, finish, floor, go against, go counter to,
   interfere with, lock horns, make a rebuttal, meet head-on,
   militate against, nonplus, oppose, oppugn, overthrow, overturn,
   overwhelm, parry, put to silence, rebut, reduce to silence, refute,
   rejoin, resist, run against, run counter to, settle, shut up,
   silence, smash all opposition, squash, squelch, subvert, surrebut,
   surrejoin, swim upstream, undermine, upset, work against