The 36-year-old's first half tap-in in Germany's 7-1 semi-final thrashing of Brazil took his tally to 16 goals in the competition - one ahead of the former Barcelona and Real Madrid star.
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As a result, Mourinho was disappointed to see the former Barcelona and Real Madrid star lose his tournament record and revealed there is only one player he rates more highly than the Brazilian in the game's history.
"Hats off to Klose," Mourinho said to Yahoo. "I highly respect the numbers he has achieved but the truth is that a player who I consider the best after Maradona lost a record.
"I believe that Ronaldo was the best player of the last two decades - at least he doesn't lose the title of being the best of the past 20 years."
Mourinho worked with Ronaldo during his solitary season at Barcelona in 1996-97, as part of Bobby Robson's coaching staff, with the 37-year-old scoring 34 goals in 37 games at Camp Nou.