The former Manchester United manager surprisingly recorded a video message to the unemployed Frenchman, who received the Lifetime Achievement Award at the glitzy ceremony in Monaco.
The pair were often at each other’s throats when they competed at the biggest Prem clubs.
Former Arsenal boss Wenger famously pushed Mourinho on the Stamford Bridge touchline during his second stint in charge of Chelsea.
It got nasty at times in the media with Mourinho calling Wenger a “specialist in failure” and a “voyeur”.
Mourinho said: “There were some episodes along the road. “I can only speak by myself. I really enjoyed the competition. But the real respect is always there. He made lots of history in that football club.
Wenger was recognised with the special honour for his three Prem titles and seven FA Cup victories during 22 years in North London.
There was also acknowledgement of the 2003-04 season in which Arsenal won the title without losing a Prem match.
Mourinho, 56, said: “The nickname is there – the Invincibles. Amazing. A coaching philosophy, the almost perfect team.”