Oldham had lost any chance of reaching the play-offs with a terrible run which saw them take just one point from a possible 15 in April, while Scunthorpe's improvement late in the season had lifted them to the safety of mid-table.
The lack of incentive showed but Scunthorpe were the much livelier team and carved out a number of chances as they dominated the second half.
Oldham were off colour, finishing their season without a win in seven games after Billy Sharp equalised in the closing minutes.
Latics veteran David Eyres had broken the deadlock with his second goal of the campaign as Oldham went ahead against the run of play.
Eyres, at 42 the oldest player in the whole of English professional football, is now out of contract at Boundary Park but plans to continue his career whether or not Oldham give him a new deal.
Home manager Ronnie Moore used the match to give a debut to 17-year old right-back Neal Eardley, a Wales youth international, who coped well with his first taste of league action.
But Scunthorpe's Sharp and strike partner Andy Keogh were a handful and it was no surprise when the Iron drew level.
Earlier, the visitors had a good chance to go in front when pacey winger Cleveland Taylor crossed from the right and Keogh shot straight at keeper Lee Grant from 10 yards.
Grant, making his last appearance for Oldham on loan from Derby County, had little else to do in the first half but Scunthorpe keeper Tom Evans was also unemployed until the 44th minute.
Evans watched a Paul Warne shot fly over the bar before Oldham grabbed the lead in first half injury time.
Eardley's pass found Richie Wellens on the edge of the box and his cross was controlled by Eyres who cut inside from the far post and blasted home from 10 yards.
Scunthorpe almost equalised on 48 minutes as midfielder Matt Sparrow brought a great save from Grant.
Their equalising goal came on 88 minutes as substitute Steve Torpey flicked on to Sharp and he volleyed home his 23rd goal of the season from six yards.