Parkinson's men were heading for their third straight win in all competitions when Gillingham netted a barely-deserved leveller deep into injury time through substitute Antonio German.
With City looking comfortable for large periods of the match and Gillingham offering little as an attacking force throughout the contest, the added time goal for the visitors was understandably a bitter pill to swallow for Parkinson and his players.
Clearly disappointed after having victory snatched from his team's grasp, Parkinson felt the Bantams were ultimately left to rue their inability to net an all-important second goal when they were in the lead.
Parkinson said: "It (the equaliser) has knocked the stuffing out of us really because it is a game we should have won.
"I felt we had enough chances, especially in the second half when we'd gone one up, to kill the game off.
"We should have been out of sight really. We've hit the post and had some other great situations where a better final pass would have resulted in another chance or two for us.
"We have to be more clinical and kill teams off. If we'd taken our chances, the game would have been dead and buried long before their goal.
"It was obviously frustrating to concede the way that we did. We know Gillingham have a threat from set-pieces but we handled that well until one moment at the end has cost us.
"It is a disappointed dressing room but I can't fault the way we approached the game.
"We perhaps gave Gillingham a bit too much of the ball at times in the first half but we were a lot more positive in the second half.
"Dividing lines are so tight in this game, however, and we need to see games through.
"We didn't finish them off and show that ruthless edge. We've had enough chances in the game but we didn't take them."
In-form Filipe Morais came off only 18 minutes into the match after injuring his shoulder, with Parkinson confirming the Portuguese winger would need an x-ray to check out the issue.
Parkinson also revealed Jon Stead wasn't injured, however, when he was replaced by James Hanson twenty minutes from the end. Parkinson simply suggested that City needed a fresh player on the pitch after Stead had put a hard shift in for the team.
Parkinson added: "He (Filipe Morais) has gone for an x-ray on his shoulder. We are hoping it isn't too bad.
"With Jon, we just needed some fresh legs out there. The pitches are heavy at this time of year and it can be a difficult surface to run on and play on so we just went with some fresh legs."
With Hanson coming off the bench for Stead, it left new loan signing Francois Zoko as an unused substitute.
Parkinson continued: "We hope he will be a good signing for us. We can at least have a look at him until January and then assess it from there.
"I felt we needed another striker in the building.
"We only met him first on the Thursday and then the deal was completed today so he hasn't really trained with the lads yet. He had a chance to them today and we put him on the bench today (Saturday). We'll have a proper look at him in training this week."