On-loan Neil MacKenzie played in Peter Till out on the right flank, he found Billy Sharp whose low cross was tucked away by the incoming Keogh.
The link-up play between the two 19-year-old players, Sharp and Keogh, was the outstanding feature of their team's hard-earned victory.
Aldershot had plenty of possession and often put their opponents on the back foot, but badly lacked the crucial cutting edge in front of goal.
Gary Holloway, Nick Crittenden and Ahmed Deen passed up decent chances, and it was left to full-back Darren Barnard to deliver Aldershot's best effort with a powerfully struck 25-yard drive in stoppage time, which demanded a fine save from the recalled Tommy Evans, reinstated to the Scunthorpe goal after 18 months in the reserves.
Overall, Aldershot keeper Nikki Bull was the busier of the two with his second half saves from Sharp, Keogh and defender Andy Crosby, enabling the Shots to stay in with a chance.
In the last two seasons, Scunthorpe have pulled in around £900,000 from the competition and, a year ago, gave Chelsea a few problems before going down 3-1 at Stamford Bridge.