His second of the evening marked his 100th in the competition, as only the second player to achieve the feat after Real Madrid's Cristiano Ronaldo.
"When you have the opportunity to make a great compliment to Messi, it is right," Conte said after the game, as quoted by BBC Football. "It is right to recognise a super super super top player.
"He is able to score 60 goals every season. I am very pleased to have had the opportunity to give him my compliment. We are talking about an extraordinary player - the best in the world.
"He wants to stay in Barcelona until the end of his career and this is the best for him, he is writing a great story for Barcelona with his team-mates."