A one-liner:

perl -lnae 'print unless $seen{$F[0]}++' < file2.txt > file1.txt
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Update: The OP needed the last entry if there are duplicates, the above solution took the first entry. Here's an alternative solutionthat requires module Tie::Hash::Indexed to be installed:

$ perl -MTie::Hash::Indexed -lane '\
  sub BEGIN {tie %seen, "Tie::Hash::Indexed"};\
  sub END {print $seen{$_} for keys %seen};\
  $seen{$F[0]} = $_'  file2.txt > file1.txt
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