His timing was 0.58 seconds slower than the qualification mark for the finals.
Commenting on his performance, having shaved off five seconds from his Olympic qualification time, the 21-year-old said, "I am really proud of my performance today. It's disheartening to have missed the finals by such a small margin but I could not have gone any faster."
Sharath, who is to participate in four events at the Paralympic Games - 100m Butterfly, 100m Breaststroke, 50m Freestyle and 200m IM - has just returned from a high-performance training camp at the University of Western Australia, Perth.
There, he trained under the watchful eye of Mel Tantrum, a Gold Licensed high-performance swimming coach, a program funded by the GoSports Foundation and its network.
Sharath will next swim the 100m Breaststroke, his pet event, on September 1.