Clarke guided home in the opening exchanges of the game to give the Shakers the advantage.
Latics did forced chances through Matt Palmer and Carl Winchester but both were halted by the hands of the Bury goalkeeper.
Athletic huffed and puffed for a leveller but it was Bury who stole the points from SportsDirect.com Park, leaving Latics in 23rd position.
John Sheridan made changes to his starting 11, most notably in attack where he brought Jonathan Forte and Dominic Poleon back in for Rhys Murphy and Jake Cassidy.
Matt Palmer was also handed his Oldham Athletic debut and he made a good impression in front of the loud and proud Latics faithful.
Latics started brightly with Mike Jones forcing his way through on goal but he slipped at the final moment.
Whilst Bury went close at the back post through Tom Pope, Latics raced up the other end and Liam Kelly shaped one wide of the post.
On nine minutes, however, Bury took the lead through striker Clarke.
A ball over the top was not dealt with by central defender James Wilson and Clarke capitalised to poke the ball beyond Joel Coleman to give the Shakers the lead.
Clarke almost doubled his and Bury’s advantage five minutes later as he shot from five yards but Coleman managed to handle on the line to deny the forward.
Latics needed some energy and a strong run from midfielder Carl Winchester lifted the crowd but his shot from 25 yards was comfortably held by Bury goalkeeper Ian Lawlor.
The pressure was with the home side and midway through the half Forte crossed into the centre but it skimmed the head of captain Liam Kelly.
Whilst Latics were enjoying much of the ball, they struggled to create clear cut chances, and it would be Bury that went close again after the half hour mark.
Clarke headed the ball down for Andrew Tutte to shoot but his volley went wide of Coleman’s goal.
Palmer, who was having an impressive start to life at the club, proved to be neat on the ball and he provided energy in the midfield.
It was the Burton Albion loanee who almost equalised five minutes before the break but his shot from 25 yards was tipped over the bar by Lawlor.
Athletic started the second half brightly as Jones cut inside from 18 yards and his deflected shot went wide for a corner.
The midfielder was taking the game to his opponents and on 50 minutes had a free kick in a similar position to his goal against Millwall.
He lined the ball up but his up and under free kick was well saved by goalkeeper Lawlor.
Whilst Latics were dominating the open proceedings, they were almost caught on the counter attack as Coleman punch fell to the path of Clarke but Danny Lafferty was back to clear off the line.
Winchester was the next man to force the goalkeeper into a save, albeit a fortuitous one. He powerfully struck from 25 yards which forced the goalkeeper to save his knees.
Jones’ set piece deliveries were causing Bury’s defence to back off, and Timothee Dieng almost capitalised at the back post but the ball went wide.
With 20 minutes of the game remaining, Latics were let off after a mix up in the defence.
Clarke was presented with too much space in the centre and he fed the ball into the path of Tutte but he hit the crossbar from 12 yards.
Two minutes later, there were huge shouts for a penalty as Dieng was being manhandled in the area but the referee was unmoved.
Latics were pushing but Bury’s defence were standing firm and keeping Latics out, despite Cassidy and Murphy joining the action.
With time running out, Latics launched long balls into the area but to no use and it was Bury that came away from SportsDirect.com Park with the win.
Oldham Athletic: Coleman, B.Wilson (Cassidy 68’), J.Wilson, Dieng, Lafferty, Kelly, Jones, Winchester, Palmer (Croft 88’), Forte, Poleon (Murphy 74’).
Subs not used: Cornell, Mills, Edmundson, Vassell.
Bury: Lawlor, Hussey, Tutte (Jones 74’), Clarke, Etuhu, Clarke, Mayor (O’Sullivan 46’), Pope (Rose 79’), Soares, Pugh, Brown.
Subs not used: Mellis, Burgess, Lowe, Miller.
Goals: Oldham Athletic 0-1 Bury (Clarke 9’)
Attendance: 5,537 (1,237 visiting supporters)