Rathore, Athens Olympic silver medalist in men's double trap, and Anjali, former 10m air rifle world number one, will now miss London Olympics as the competition in Doha is the last qualifying event for them.
Double trap world number two Ronjan Sodhi, who had already earned his London Olympics quota, too could not make it to the final round, adding to the gloom in the Indian camp.
All eyes were on Rathore after he had equalled the world record of 148/150 at Asian Shotgun Championship in November, but he failed to adjust to the windy conditions.
After enjoying near perfect conditions during training, the weather this morning made life difficult for all shooters with high wind speeds playing havoc.
Banking on his experience, Rathore opened with a 48/50 that tied him for the lead. But it all came undone in the second series as he could manage only a 41. With his back to the wall, Rathore needed to shoot at least 47 to be in contention for the final round but he ended with a 46 for a final total of 135/150
"It was apparent what went wrong. The gusts of wind were just too much to handle. That 41 in the 2nd round was the problem. We have ways to adjust technically but those ways are to cope up, not to overcome the conditions. The wind was about 22 miles, the gusts were 27 miles. It was moving the gun," said Rathore in disappointment.
"Training had been fantastic. There is time and then there is effort both have to be balanced out. For that you need to be in the team and training and competing. I knew I had just one chance and it is touch and go in these circumstances," he said.
Sodhi had two rounds of 46 but his final round of 42 proved disastrous as he finished with 134.
"The conditions just changed today and we could not adapt to it as we had not trained for this. It took us by surprise. I am disappointed at not making the final. Every competition is crucial but I had earlier said that I was using this event to experiment a bit keeping the Olympics in mind. This situation could arise in Olympics as well and now I will have to keep this scenario in mind as well and train accordingly," said Sodhi.
The other Indian in the fray in double trap, Mohd. Asab finished with 135, the same score as Rathore. The shoot-off for the final was at the score of 136.
The Indian team of Rathore, Asab and Sodhi won the team bronze with a total of 404. UAE, which had all their three shooters in the final, won the team gold.
Anjali rolled back the years with 396/400 to put herself in contention for a place in the final. She has been on the comeback trail since last year after motherhood and it was a creditable performance as she was shooting with a borrowed barrel after her gun broke down. Her teammate Ayonika Paul also shot 396. That put both the shooters in a 7-way shoot-off for four final spots.
In the shoot-off, Anjali shot 50.3 to finish fifth and just missed out on a place in the final. The women's team of Anjali, Mampi Das and Ayonika Paul settled for silver.
On a day of disappointment for the Indians, Shayan Masood won the gold in the junior category on his 17th birthday while world junior champion Asher Noria won a bronze. However, this result will not be recognized due lack of sufficient entries.