ha_innodb.cc:

  Update the InnoDB internal auto-inc counter in ::write_row() if the statement is a REPLACE that fails in a duplicate key error: REPLACE will handle duplicate key error, and the insert will eventually succeed; note that we did NOT change InnoDB's behavior in an UPDATE, because updating the auto-inc counter in an UPDATE would require a bigger patch (Bug #11005)

sql/ha_innodb.cc

@@ -3221,6 +3221,23 @@ ha_innobase::write_row(
           	}
         }
 
+        /* A REPLACE command and LOAD DATA INFILE REPLACE handle a duplicate
+        key error themselves, and we must update the autoinc counter if we are
+        performing those statements. */
+
+        if (error == DB_DUPLICATE_KEY && auto_inc_used
+            && (user_thd->lex->sql_command == SQLCOM_REPLACE
+                || user_thd->lex->sql_command == SQLCOM_REPLACE_SELECT
+                || (user_thd->lex->sql_command == SQLCOM_LOAD
+                    && user_thd->lex->duplicates == DUP_REPLACE))) {
+
+                auto_inc = table->next_number_field->val_int();
+
+                if (auto_inc != 0) {
+                        dict_table_autoinc_update(prebuilt->table, auto_inc);
+                }
+        }
+
 	innodb_srv_conc_exit_innodb(prebuilt->trx);
 
 	error = convert_error_code_to_mysql(error, user_thd);