The Socceroos, fielding only four survivors from the team that booked their ticket in Qatar at the weekend, were frustrated by the pacy visitors and needed second-half goals to grind them down.
Mile Sterjovski broke the deadlock in the 55th minute after he punished a defensive error inside the six-yard box and beat goalkeeper Sayed Mohamed for his eighth international goal. David Carney doubled the lead in the 88th minute after Jason Culina's spectacular overhead kick ricocheted off an upright for Carney to ram the ball home.
Bahrain had the ball in the net during the second half from an Abdulla Marzooq header, but the defender was ruled offside. It would have been the first time Australia had conceded a goal in their last seven qualifying games.
Australia hold on to their lead at the top of Group A and will play regional rivals Japan in Melbourne next Wednesday, with both teams already through to the FIFA World Cup finals.
The Socceroos could have had a third but incredibly the ball stayed out after Harry Kewell and Sterjovski had goalbound chances blocked on the line in the 75th minute. But for the most part, in front of just under 40,000 fans at a half-filled Olympic stadium, the Australians struggled to get into gear.
The surprise omissions from the Australia team were English Premier League stars Tim Cahill and Vince Grella, with Cahill left out entirely and Grella on the bench. Grella came on in the 62nd minute. Coach Pim Verbeek said Cahill had stiff muscles and would not be risked.
Bahrain, needing a point to lock up third spot in the group and with it a potential World Cup play-off against Oceania champions New Zealand, looked the livelier in the first half. Skipper Mohamed Salmeen had a free header off an Abdulla Abdi corner in the 24th minute but the chance went over the bar.
Celtic striker Scott McDonald had a glorious chance to break his international goal drought in his 12th game minutes later after being put clear by Brett Holman but he blazed his volley over the bar for the hosts.
Bahrain continued to press and Mahmood Abdulrahman's free-kick was flicked on, only for goalkeeper Mark Schwarzer to fumble the ball and regather at the second attempt on his line.
Sterjovski had a free header comfortably taken by goalkeeper Sayed Mohamed before Salman Isa blazed just over the bar nearing half-time.