Socceroos do the business in Canberra
The three points keeps Australia in second place in Group B and one step close to progression into the next round of World Cup qualifying.
Australia could have taken the lead in the opening two minutes but Cahill's acrobatic effort was brilliantly saved.
The Socceroo legend came even close shortly afterwards but his shot from Aaron Mooy's saved strike came off the crossbar.
Tomi Juric was forced off with injury on the half-hour mark, with Nathan Burns coming on in his place.
Burns was straight into the thick of the action and on 39 minutes won a penalty after his tricky feet drew a foul in the area.
Skipper Jedinak stood up and smashed the penalty to his right to give Australia a deserved lead.
Cahill doubled the lead five minutes into the second period after a sublime pass from Mooy put him in on goal.
Mooy was involved in the third as well, with his dangerous corner-kick headed into the net by a Kyrgyzstani defender.
Pavel Matiash, the Kyrgyzstan goalkeeper, pulled off a number of great saves to deny the Socceroos a fourth goal in stoppage time.