Matthew Kilgallon put the Bantams ahead with a looping header only for Scunthorpe United to cancel out his opener within four minutes through Conor Townsend.
It was enough to ensure the Iron finished fifth, in the process confirming a two-legged semi-final tie with Rotherham United.
City had looked to also be on course to extend their season when the new year dawned only for a six-game losing run to kill off those hopes.
Grayson has been unable to turn that slump around sufficiently but the season did at least end on a positive.
The visitors took the lead 11 minutes into the second half when Matthew Kilgallon met Tony McMahon’s corner with a header that looped beyond Matt Gilks in the home goal.
Up to that point, the game had been a dour affair with the first half’s only moment of note coming when Josh Morris curled a free-kick against his old club’s crossbar.
KIlgallon’s opener, however, sparked the hosts into a near instant response as Conor Townsend equaliser on the hour.
Neat play by substitute Tom Hopper saw the ball worked to Neal Bishop on the edge of the area and he, in turn, found Townsend on the overlap.
After his initial shot was blocked, the left back made no mistake with the follow-up.
Charlie Wyke came agonisingly close to winning it for Bradford with a thunderbolt of a shot that crashed against the underside of the bar nine minutes time before goalkeeper Matt Gilks snatched the ball ahead of the advancing Matt Gilks.
Grayson said: “Killa only needs the winning lottery tickets tonight and it will round off a good week!
“The awards the other night were rightly deserved because of how well he’s done since I’ve been here and before that.
“It was a great ball from Macca (Tony McMahon) and he rose really well. It was nice to see it hit the back of the net.
“He’s an experienced player and he’s good to have around the dressing room.
“We said to the players we didn’t want to let the last game of the season peter out and they didn’t.
“I thought it was a decent game and the players can be a little disappointed we didn’t win.”