Consider a temp table which would be exact replica of your final table, cleaned out with each run:
engine = create_engine('postgresql+psycopg2://user:pswd@mydb')
df.to_sql('temp_table', engine, if_exists="replace")
sql = """
UPDATE final_table AS f
SET col1 = t.col1
FROM temp_table AS t
WHERE f.id = t.id
"""
with engine.begin() as conn: # TRANSACTION
conn.execute(sql)