The visitors were under pressure for much of the game against a Scunthorpe team that created a number of chances without being able to finish in front of goal.
Leading marksman Billy Sharp could have had at least a hat-trick to add to his five-goal tally this season.
He was denied by a linesman's flag in the 11th minute when he netted from close range following a cross from Cleveland Taylor.
He then fizzed a couple of cracking efforts across the face of goal and just wide of the far post.
His luck didn't change in the second half with a header from a corner cleared off the line by Cheltenham midfielder Grant McCann.
And finally he was denied again by a save at full-stretch from keeper Shane Higgs who took man-of-the-match honours for the visitors.
Higgs rescued his side again with a point-blank save to deny Scunthorpe winger Ian Morris as it threatened to be an afternoon of frustration for the hosts.
Cheltenham offered little as an attacking force with a free-kick from McCann curling just wide being their best effort of the first half.
They forced just one save from keeper Joe Murphy when he had to be alert just after the break to touch over a looping header from Steve Guinan.
It was a real backs to the wall effort by the visitors who were looking for their first away point since the opening day of the season.
It seemed they may hang on to one until the last minute when Keogh weaved his way into the box and finished decisively with a low shot into the bottom corner to give Scunthorpe a second successive home win.