Aguero completed a move to the Etihad Stadium from Atletico Madrid in July for a fee of £38m and Messi believes that it is money well spent.
"There is no doubt in my mind that City have signed an exceptional player," said 24-year-old Messi.
"He will give them a real cutting edge. He's unique and has immense power, strength and an incredible work ethic. He will certainly stand out in terms of what he will bring to City.
"Defenders will find it so difficult to play against him.
"Personally I would loved to have seen him in stay in Spain and preferably move to Barcelona."
Aguero, 23, could be in line to make his City debut against Swansea City on Monday night.