I currently hold a B1 US Visa on my Indian passport and I will be travelling to the US soon. However, I will be taking a flight from Sydney instead of India and I have booked one from Qantas. I do understand that Australia comes under the visa waiver program but India doesn't. However, Qantas is continuously poking me to complete ESTA. I am confused as ESTA is a substitute for visa. Am I missing something here or do I need to fill ESTA even though I have a valid visa.
ESTA is only necessary if you want to travel to the US under the Visa Waiver Program. As you have a valid visa, ESTA is not necessary.
Have you entered your visa information into the Quantas booking system, so that they actually know about your visa? If not, then it explains the poking, since they have to assume you want to use the VWP to travel. If you have, then their IT system might not differentiate and just shows the ESTA notices for every traveller to the US.
There's nothing wrong with Dunni's answer, but I'd add - as a holder of a US B1/B2 visa despite having a Visa Waiver country citizenship - that airlines who deal primarily with VWP passengers to the US have varying degrees of success dealing with visa holders.
BA recently (finally!) improved their system to the point that I can use both online checkin and automated bag drop. The automated bag drop at LHR T5 is, in fact, manned at the entry to the area, and it's the people there who inspect my visa. However, BA remain apparently unable to record that I have a ten-year visa, in order that I don't have to do this every time I fly.
US airlines I've tried to fly from the UK to the US are generally unable to deal with it at all, and say I cannot even use online checkin but must do everything manually at the airport. Admittedly, I haven't used any such for a couple of years.
And as for code share flights, where you use one airline's checkin system to gain access to another airline's plane, forget it; I've never found this to be properly handled. As soon as I can't give them an ESTA number, everything falls over hard.
The point of this (slightly ranty) answer is that I suspect you've run into a very common stumbling block with airlines the vast majority of whose passengers will be travelling on ESTA, and there may simply be no way around it. You should still be able to buy a confirmed ticket, but may find that you can't do anything else in advance of travelling, and must fall back to manual procedures at the airport for all other functions (checkin, seat allocation, bag drop, etc.). Sorry.