BUG: Fixed DataFrame.combine with non-unique columns

doc/source/whatsnew/v3.0.0.rst

@@ -1234,12 +1234,12 @@ Other
 - Bug in printing a :class:`DataFrame` with a :class:`DataFrame` stored in :attr:`DataFrame.attrs` raised a ``ValueError`` (:issue:`60455`)
 - Bug in printing a :class:`Series` with a :class:`DataFrame` stored in :attr:`Series.attrs` raised a ``ValueError`` (:issue:`60568`)
 - Deprecated the keyword ``check_datetimelike_compat`` in :meth:`testing.assert_frame_equal` and :meth:`testing.assert_series_equal` (:issue:`55638`)
+- Fixed bug in :meth:`DataFrame.combine` with non-unique columns (:issue:`51340`)
 - Fixed bug in :meth:`Series.replace` and :meth:`DataFrame.replace` when trying to replace :class:`NA` values in a :class:`Float64Dtype` object with ``np.nan``; this now works with ``pd.set_option("mode.nan_is_na", False)`` and is irrelevant otherwise (:issue:`55127`)
 - Fixed bug in :meth:`Series.replace` and :meth:`DataFrame.replace` when trying to replace :class:`np.nan` values in a :class:`Int64Dtype` object with :class:`NA`; this is now a no-op with ``pd.set_option("mode.nan_is_na", False)`` and is irrelevant otherwise (:issue:`51237`)
 - Fixed bug in the :meth:`Series.rank` with object dtype and extremely small float values (:issue:`62036`)
 - Fixed bug where the :class:`DataFrame` constructor misclassified array-like objects with a ``.name`` attribute as :class:`Series` or :class:`Index` (:issue:`61443`)
 - Fixed regression in :meth:`DataFrame.from_records` not initializing subclasses properly (:issue:`57008`)
-
 .. ***DO NOT USE THIS SECTION***
 
 -

pandas/core/frame.py

@@ -9041,9 +9041,9 @@ def combine(
         new_columns = self.columns.union(other_columns, sort=False)
         do_fill = fill_value is not None
         result = {}
-        for col in new_columns:
-            series = this[col]
-            other_series = other[col]
+        for i, col in enumerate(new_columns):
+            series = this.iloc[:, i]
+            other_series = other.iloc[:, i]
 
             this_dtype = series.dtype
             other_dtype = other_series.dtype

pandas/tests/frame/methods/test_combine.py

@@ -45,3 +45,17 @@ def test_combine_generic(self, float_frame):
         )
         tm.assert_frame_equal(chunk, exp)
         tm.assert_frame_equal(chunk2, exp)
+
+    def test_combine_non_unique_columns(self):
+        # GH#51340
+        df = pd.DataFrame({"A": range(5), "B": range(5)})
+        df.columns = ["A", "A"]
+
+        other = df.copy()
+        df.iloc[1, :] = 11
+
+        def combiner(a, b):
+            return b
+
+        result = df.combine(other, combiner)
+        tm.assert_frame_equal(result, other)