Bury's penalty loss to Stoke City at the bet365 Stadium means City now are guaranteed at least a top two finish in Northern Group C.
After the game finished 1-1 after normal time, Stoke won the resulting shoot-out 4-3 to claim the bonus point on offer.
The result means Bury finish their campaign on four points while Stoke end up with two.
City, currently on six points, now only need a draw, or a loss by less than a two-goal margin, at Morecambe on Wednesday evening to secure top spot in the group.
Teams who finish top of their respective groups are guaranteed a home draw against side who claimed second spot in their own group.
The draw for round two of the Checkatrade Trophy will take place on Thursday (10 November 2016) on Sky Sports News HQ from approximately 10:30am.
The draw will be regionalised , meaning City will face another side from the northern section in the knock-out stages.
Round two matches will take place the week commencing the 5 December.