The German midfielder found the net in the ninth and 73rd minutes on Sunday while Argentine teenager Claudio Etcheverri also fired home a free kick and Erling Haaland a penalty before the break.
Substitutes Oscar Bobb and new signing Rayan Cherki sealed the emphatic victory in the last 10 minutes to draw City level on goal difference with Juventus, who beat Wydad Casablanca 4-1 earlier on Sunday.
City and Juventus meet in their final group match in Orlando on Thursday to decide which of them progresses to the round of 16 as group winners.
“A really good performance,” said Gundogan. “I think we had our moments in the first half, and then also the second part of the second half.
“I think the result speaks for itself, and in the end, fully deserved.”
City manager Pep Guardiola illustrated the depth of his squad by making 11 changes, and Gundogan made the most of his start by opening the scoring with a chipped cross that floated over the head of Al-Ain keeper Khalid Eisa and into the net.
Al-Ain were showing more ambition than they had in their 5-0 loss to Juventus and winger Nassim Chadli had a chance to equalise in the 15th minute but City keeper Stefan Ortega Moreno managed to push it wide.
Etcheverri, making his first start for City, doubled the lead in the 27th minute when he bent a free kick around a poorly-placed defensive wall and past the hapless Eisa.
Haaland almost immediately created a chance for himself by dispossessing the final defender but he took the ball too wide to get around Eisa and his shot went across the goal.
The big Norwegian went through on goal again in the 41st minute before again angling his shot wide of the far post but made no mistake from the spot with his third chance to score in first-half stoppage time.
Egyptian Ramy Rabia wrestled Manuel Akanji to the ground from a corner and after VAR informed the referee of the offence, Haaland sent Eisa to the left and banged the ball into the right-hand corner for his 32nd goal of the season.
City kept up the pressure in the second half and forward Matheus Nunes turned and volleyed the ball past the post just after the hour mark before Eisa finally showed his quality by twice denying Haaland from close range.
Chadli had another chance in the 69th minute but fired his shot high over the bar and Gundogan soon ended any hopes of a comeback with his second goal.
Bernardo Silva drifted across the edge of the box before drilling a pass towards the penalty spot and Gundogan got a great first touch to take him past the defence before lifting the ball over Eisa.
Bobb cut inside the box onto his left foot to beat Eisa at his near post eight minutes from time before his fellow winger Cherki sealed the rout with a clinical finish from the edge of the box. (Reuters)
