The Ukrainian shot 106.4 in the final for a 706.4 total, ahead of France's Raphael Voltz, who won silver in a shoot-off with James Bevis of Great Britain.
It proved to be a tense climax, with Kovalchuk delaying his aim as he claimed the title with his final shot.
'The last shot was decisive,' he admitted. 'At the beginning I wasn't very successful. I mounted the gun, I didn't feel confident. I postponed my shot and then mounted the gun again. I was sure that the shot would be the right one and it was.'
In the afternoon session, Cedric Fevre shot a new world record to claim gold in the Mixed R3-10m Air Rifle Prone - SH1.
The Frenchman shot 106.7 in the final to claim an overall 706.7 total, which eclipsed the previous best mark to edge out Britain's Matt Skelhon into silver-medal position.
Chinese shooter Zhang Cuiping - who claimed the first gold medal of the London 2012 Paralympic Games by setting a new world record in the women's R2-10m Air Rifle Standing - SH1 on the opening day of action - took bronze this time.
The Royal Artillery Barracks witnessed perhaps the final hurrah for Australian veteran Elizabeth Kosmala, who admitted she may now bow out of the Paralympic arena.
The 70-year-old competed at her first Games in 1972 in Heidelberg and is the oldest competitor at London 2012.
After failing to qualify for the Mixed R3 10m Air Rifle Prone - SH1 final, she admitted: 'It is all over now, maybe for ever and ever. I think it will be.
'I have participated in 11 Games. It's wonderful, I love it, but you've got to be getting medals to keep coming away (from home). It is getting tougher and tougher.
'I have got two grandsons and I would like to spend more time with them. I would like to see more of Australia with my husband, because I have seen a lot of the world but not of Australia.