Here how I solved this problem, sharing it so that if someone else also face this issue then it will be helpful for him I am loading the two datasets separately and then registering them as temp table and now I am able to run the join query using those two tables. Below is the sample code.
String table1 = "TABLE_1";
Map<String, String> map = new HashMap<>();
map.put("zkUrl", ZOOKEEPER_URL);
map.put("table", table1);
Dataset<Row> df = sparkSession.sqlContext().load("org.apache.phoenix.spark", map);
df.registerTempTable(tableName);
String table2 = "TABLE_2";
map = new HashMap<>();
map.put("zkUrl", ZOOKEEPER_URL);
map.put("table", table2);
Dataset<Row> df2 = sparkSession.sqlContext().load("org.apache.phoenix.spark", map);
df2.registerTempTable(table2);
Dataset<Row> selectResult = df.sparkSession().sql(" SELECT * FROM TABLE_1 as A JOIN TABLE_2 as B ON A.COLUMN_1 = B.COLUMN_2 WHERE B.COLUMN_2 = 'XYZ' ");
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