The Santiago Bernabeu side have won three European titles over the past four seasons following their most recent success and some have suggested their current crop of players is among the best ever.
Nevertheless, Koeman believes Barcelona were on another level during Guardiola's spell in charge between 2008 and 2012.
"Real Madrid are the champions. They have been the best team in the Champions League this season and they played an excellent second half against Juventus in the final," the Everton manager told reporters.
"But I do not think they can be compared with the Barcelona of Pep.
"That was an excellent team."
Barcelona lifted the Champions League two times during Guardiola's four-year spell, beating Manchester United in both 2008-09 and 2010-11.