Substitute Ryan Flynn opened the scoring in first half injury time converting from close range to give Latics the lead.
Wigan Athletic loanee Billy Mckay extended Athletic’s lead early in the second half as he clinically converted from 12 yards to give Latics a cushion.
Athletic dominated the game but come under late pressure as Doncaster Rovers reduced the arrears from the penalty spot.
Liam Mandeville sent Connor Ripley the wrong way to make the scores 2-1 and Latics held on to secure their place in the hat for the second round draw on Monday, November 7.
Stephen Robinson made a couple of changes to his side as Ollie Banks came into the side for his first start in over two months.
It took the game a while to kick in but it would be Latics that dominated the opening 45 minutes.
However, it would be the visitors who should have taken the lead on five minutes.
Liam Mandeville got beyond his man on the left, fired across the box but Matty Blair could not convert at the back post.
Latics were dealt an early blow as Carl Winchester hobbled off on eight minutes with an injury to be replaced by Flynn.
Athletic then started to grow into the game with Ryan McLaughlin a constant threat on the right hand side.
On 15 minutes his cross into the box found Lee Erwin at the back post but the Leeds loanee just stabbed his effort past the far post.
Athletic were dealt a further blow before half an hour as Paul Green hobbled off against his former club with an injury.
Ousmane Fane replaced the midfielder as Latics started to really take a grip on the game going forward.
McLaughlin’s crosses were really causing a problem for the Doncaster defence but they just could not unfortunately fall into the path of a Latics man.
Athletic almost took the lead on 34 minutes as Mckay fed the ball into the path of Erwin from 25 yards but Marko Marosi made the save.
Latics were playing some excellent football with Ollie Banks and McLaughlin at the centre of the action.
The pair combined as McLaughlin created a crossing opportunity but Mckay’s header was just blocked.
With half time approaching, Latics did manage to make the breakthrough as Flynn put Robinson’s men ahead.
Charles Dunne’s cross into the box found Peter Clarke in the centre who nodded into the path of the onrushing midfielder and he made no mistake from three yards.
Athletic were playing with confidence and they took that form into the second half where they were a constant threat.
It took Latics eight second half minutes to extend their lead and a great finish it was.
Flynn broke excellently from midfield, played the ball into the path of Mckay who made no mistake from 12 yards as he cooly slotted into the bottom corner under pressure.
That was a big goal for Latics as it calmed the nerves around SportsDirect.com
It was almost three on the hour mark as Erwin’s fierce strike was partially saved by the goalkeeper but Mckay could not convert the follow up.
Athletic calmly took control with the opposition forced to chase the game to get something out of it.
However, they were met by a stubborn Oldham Athletic defence who were determined not to concede.
They were calved open on 70 minutes, though, with Blair racing through one-on-one with Connor Ripley but the striker fluffed his lines and shot wide.
Athletic could have put the game beyond doubt in the final 10 minutes as Flynn evaded his man, raced through with the goalkeeper but slipped his shot wide of the goal from the edge of the box.
Robinson’s men did come under intense pressure in the final minutes of the game with Doncaster throwing men forward in a bid to get something out of the game.
Four minutes into six minutes of additional time, Doncaster Rovers won themselves a penalty as Marquis was adjudged to have been held back.
Mandeville stepped up to take the penalty and sent Ripley the wrong way to reduce the arrears.
In a nervy ending, it would be Latics who almost grabbed the fourth of the game, and their third as Mckay charged down goalkeeper Marosi but the ball fell inches wide of the post.
After a barrage of attacks from the opposition, Latics did see the game out well and are in the hat for the second round of the competition.
Oldham Athletic: Ripley, Dummigan, Clarke, Burgess, Dunne, Winchester (Flynn 9’), Green (Fane 28’), Banks, McLaughlin, Erwin (Law 77’), Mckay.
Subs not used: Kettings, Wilson, Osei, Jahraldo.
Doncaster Rovers: Marosi, Alcock, Garratt (Evina 46’), Baudry, Marquis, Middleton (Keegan 57’), Wright (Butler 63’), Blair, Mandeville, Beestin, Richardson.
Subs not used: Etheridge, Longbottom.
Goals: Oldham Athletic (Flynn 45+1’, Mckay 53’) 2-1 Doncaster Rovers (Mandeville 90+4’)