Messi scored his first goal for Paris St Germain to help secure victory over City in their Group A clash at Parc des Princes on Tuesday night.
PSG took the lead in the seventh minute when City failed to clear a cross into the box and Idrissa Gueye crushed the ball in the top corner.
City nearly secured an instant equalizer as Raheem Sterling headed against the crossbar, before Bernardo Silva returned the free ball to the bar as he looked certain he would score.
Messi, returning from a knee problem, capped a fine overall performance when he played a one-two with Kylian Mbappe at the edge of the penalty area and had a magnificent finish in the top corner.
And after the win, Messi congratulated City on revealing their relief at having scored their first goal for their new side.
Speaking to Canal +, Lionel Messi said: “They were great opponents. It was very important for us to win the game after our draw against Brugge. I am very happy to have scored. “
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He added: “I hadn’t been able to play recently and it was only my second game at this stadium. I adapt to my new team.
“The more we play together, the better our relationship will be. We all need to grow together, improve and keep doing our best. “
PSG move to the top of Group A after the win, with City in third place after Brugge 2-1 victory in Leipzig.
Ahead of the game, City manager Pep Guardiola said his side were “ready to suffer a bit” after Messi was named in the starting lineup.
He told BT Sport: “I have enjoyed it for years. With these types of players, we are prepared to suffer a bit. They’re unstoppable 90 minutes, too good to control all the time, not just him – Mbappe, Neymar, Verratti, we know that.
“We have an idea of the game we want to make and we try it. “