City took the lead after only two minutes as David Cotterill turned in a cross for striker Donaldson, who made no mistake with a guided finish into the bottom corner from inside the six-yard box.
Cotterill appeared in menacing form in the opening exchanges and he almost doubled the visitors' lead when he took aim from distance, only to see his long-range effort fly past the post.
In a dominant opening, it was the hosts who again threatened to extend their advantage as Donaldson profited from a pass from Jonathan Grounds, but the frontman saw his drilled effort across the face of goal flash wide.
Donaldson did not have to wait too long for another chance, however, as he turned in from close range in the 14th minute to give his side a much-deserved two-goal lead.
Having been anonymous for the much of the first half, Wigan sprung into life in the 36th minute as James McClean scored with a fine effort from outside the box to pull one back before the interval.
McClean continued his enterprise in the second half and Wigan might have found an equaliser when he produced an inch-perfect ball for defender Ivan Ramis, who headed clean over the bar.
The Irishman's efforts were not enough, though, as Donaldson completed his hat-trick in the 64th minute with a simple finish from Demarai Gray's cross to wrap up all three points for the Blues on home soil.