diff --git a/spark/src/main/scala/io/delta/tables/DeltaMergeBuilder.scala b/spark/src/main/scala/io/delta/tables/DeltaMergeBuilder.scala
index 50b9ac5b116..0d0b8e69964 100644
--- a/spark/src/main/scala/io/delta/tables/DeltaMergeBuilder.scala
+++ b/spark/src/main/scala/io/delta/tables/DeltaMergeBuilder.scala
@@ -337,7 +337,9 @@ class DeltaMergeBuilder private(
 
   private def mergePlan: DeltaMergeInto = {
     var targetPlan = targetTable.toDF.queryExecution.analyzed
-    val sourcePlan = source.queryExecution.analyzed
+    var sourcePlan = source.queryExecution.analyzed
+    var condition = onCondition.expr
+    var clauses = whenClauses
 
     // If source and target have duplicate, pre-resolved references (can happen with self-merge),
     // then rewrite the references in target with new exprId to avoid ambiguity.
@@ -346,17 +348,25 @@ class DeltaMergeBuilder private(
     // optional SubqueryAlias.
     val duplicateResolvedRefs = targetPlan.outputSet.intersect(sourcePlan.outputSet)
     if (duplicateResolvedRefs.nonEmpty) {
-      val refReplacementMap = duplicateResolvedRefs.toSeq.flatMap {
-        case a: AttributeReference =>
-          Some(a.exprId -> a.withExprId(NamedExpression.newExprId))
-        case _ => None
-      }.toMap
-      targetPlan = targetPlan.transformAllExpressions {
-        case a: AttributeReference if refReplacementMap.contains(a.exprId) =>
-          refReplacementMap(a.exprId)
-      }
-      logInfo("Rewritten duplicate refs between target and source plans: "
-        + refReplacementMap.toSeq.mkString(", "))
+      val exprs = (condition +: clauses).map(_.transform {
+        // If any expression contain duplicate, pre-resolved references, we can't simply
+        // replace the references in the same way as the target because we don't know
+        // whether the user intended to refer to the source or the target columns. Instead,
+        // we unresolve them (only the duplicate refs) and let the analysis resolve the ambiguity
+        // and throw the usual error messages when needed.
+        case a: AttributeReference if duplicateResolvedRefs.contains(a) =>
+          UnresolvedAttribute(a.qualifier :+ a.name)
+      })
+      // Deduplicate the attribute IDs in the target and source plans, and all the MERGE
+      // expressions (condition and MERGE clauses), so that we can avoid duplicated attribute ID
+      // when building the MERGE command later.
+      val fakePlan = AnalysisHelper.FakeLogicalPlan(exprs, Seq(sourcePlan, targetPlan))
+      val newPlan = org.apache.spark.sql.catalyst.analysis.DeduplicateRelations(fakePlan)
+        .asInstanceOf[AnalysisHelper.FakeLogicalPlan]
+      sourcePlan = newPlan.children(0)
+      targetPlan = newPlan.children(1)
+      condition = newPlan.exprs.head
+      clauses = newPlan.exprs.takeRight(clauses.size).asInstanceOf[Seq[DeltaMergeIntoClause]]
     }
 
     // Note: The Scala API cannot generate MergeIntoTable just like the SQL parser because
@@ -367,24 +377,9 @@ class DeltaMergeBuilder private(
     // (possible in Scala API, but syntactically not possible in SQL). This issue is tracked
     // by https://issues.apache.org/jira/browse/SPARK-34962.
     val merge = DeltaMergeInto(
-      targetPlan,
-      sourcePlan,
-      onCondition.expr,
-      whenClauses,
-      withSchemaEvolution = schemaEvolutionEnabled)
-    val finalMerge = if (duplicateResolvedRefs.nonEmpty) {
-      // If any expression contain duplicate, pre-resolved references, we can't simply
-      // replace the references in the same way as the target because we don't know
-      // whether the user intended to refer to the source or the target columns. Instead,
-      // we unresolve them (only the duplicate refs) and let the analysis resolve the ambiguity
-      // and throw the usual error messages when needed.
-      merge.transformExpressions {
-        case a: AttributeReference if duplicateResolvedRefs.contains(a) =>
-          UnresolvedAttribute(a.qualifier :+ a.name)
-      }
-    } else merge
-    logDebug("Generated merged plan:\n" + finalMerge)
-    finalMerge
+      targetPlan, sourcePlan, condition, clauses, withSchemaEvolution = schemaEvolutionEnabled)
+    logDebug("Generated merged plan:\n" + merge)
+    merge
   }
 }