Second-half goals from Mark Milligan and two from talisman Cahill gave the Socceroos nine points from three matches in Group B.
The Australians dominated the game but lacked the necessary punch up front to overwhelm the plucky home team that was full value for its 0-0 scoreline at half-time.
But once Milligan broke the deadlock 12 minutes into the second half, the result was never in doubt.
Ange Postecoglou made three changes to the team that comfortably beat Bangladesh 5-0 in Perth.
Ryan McGowan was preferred to Tarek Elrich, Matt McKay replaced Tom Rogic and Cahill came in for Nathan Burns in a 4-4-2 line-up - with a diamond midfield.
The Socceroos had the lion's share of possession in the early stages but failed to trouble goalkeeper Alisher Dodov.
McKay should have done better than shoot well over the bar when he was allowed plenty of time to pick his spot.
Massimo Luongo was the next Australian to threaten when a loose ball came to his feet but his volley from eight metres out was deflected to a corner.
McKay was again in the thick of the action after 23 minutes when Cahill nodded a high ball from McGowan to his feet but the Brisbane Roar midfielder was again off target.
The Australians were now dominating the game and were desperately unlucky not to open the scoring a few minutes later when a header from Cahill was saved by Dodov and from the ensuing action Mathew Leckie's low drive seemed destined for the back of the net but the ball was cleared on the line.
The home team however defended diligently to keep its goal intact.
It even came into the game with a flurry of attacks that raised the crowd's hopes of an upset.
Aaron Mooy was even more unlucky to hit the bar with a placed free-kick five minutes into the second half.
The Socceroos got the deserved breakthrough in the 57th minute when Mark Milligan scrambled the ball in after Tajikistan failed to deal with a Mooy corner kick.
Australia made the issue safe with another goal on 72 minutes.
Substitute Nathan Burns put McGowan through on the right with a pass into space and the fullback's low centre was flicked into the net by Cahill for his 40th goal for the Socceroos.
After Luongo was denied by the woodwork, Cahill made it three with a splendid header from a cross by substitute Tommy Oar a minute from time.
In another Group B match, Jordan beat Bangladesh 4-0 in Dhaka to stay in second spot two points behind Australia.
