Subtracting the last elements in each raw in two lists

diff = list1;
diff[[All, -1]] = Subtract[list2[[All, -1]], list1[[All, -1]]];
diff

{{1, 2, 3}, {1, 3, -2}, {2, 5, -1}}

Another solution:

list1 // ReplacePart[ {i_, 3} :> Differences[ {list1, list2}, {1, 0} ][[ 1, i, 3]] ]

{{1, 2, 3}, {1, 3, -2}, {2, 5, -1}}

Try this:

Transpose[
 Append[Transpose[list1 ][[1 ;; 2]], 
  Last[Transpose[list2 ] - Transpose[list1 ]]]]

(*  {{1, 2, 3}, {1, 3, -2}, {2, 5, -1}}   *)

Have fun!

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