The 25-year-old from Dumfries capped a brilliant performance at Zhailjau Golf Resort in Almaty by closing with a five-under-par 67 for a 24-under-par 264 total.
He won by two shots from Englishman Tom Murray, who was tied for the lead before finishing with two bogeys as he signed off with a 65.
Johnston earned £64,000 for his win in one of the second-tier circuit’s majors, lifting him 36 spots to fourth in the Road to Ras Al Khaimah Rankings.
The top 15 secure main Tour cards and the Scot, who also won the Andalucia – Costa del Sol Match Play 9 in May, is now in a strong position to earn a step up with just five events to go.
“I started the season with no category at all, and was just playing off invites,” said Johnston, who is in his first full season in the paid ranks, as he savoured his latest success.
“That first win was huge for me in taking the step on to the Challenge Tour and it seems like this one’s going to be a huge win in taking a step on to the European Tour.”
The 2017 Scottish Stroke Play champion made three cuts in his next 11 Challenge Tour events after that victory earlier in the season but picked the perfect week to rediscover his best form.
“I couldn’t even imagine this was going to happen starting this year in January with the goals that I’d set for myself,” he added after becoming the second Scot to win in Kazakhstan after Scott Henry in 2012.
Henry’s success secured him a European Tour card and now Johnston is almost certain to do likewise after clinching a fourth Scottish victory of the season on the feeder circuit.
In addition to his brace, David Law won the SSE Scottish Hydro Challenge at Macdonald Spey Valley in Aviemore while Calum Hill triumphed in the Northern Ireland Open at Galgorm Castle.
Law finished 14th in Almaty to cement his place in the top 15 in the rankings, sitting 10th, while Grant Forrest is still on course to graduate as well despite slipping to 14th after missing the cut in Kazakhstan.
Hill, who closed with a 67 to claim a share of ninth, is up to 29th, with Ewen Ferguson and Bob MacIntyre sitting 35th and 41st respectively.
Johnston, who started the final round a shot behind American Sean Crocker, opened with a bogey before getting into his stride with three birdies then making an eagle-3 at the ninth to be out in 32.
Coming home, he birdied the par-3 13th and parred every other hole.
“All week there were several times where I made bogey and then I bounced back with a birdie or two birdies, and this was just one of those weeks,” he said.
“When it’s your week these things happen, but my birdie on the second hole got me settled into the round. It just confirmed to me that ‘yeah, I am playing well, and I just need to keep on doing what I’m doing.’”
At one point in the final round, six different players co-led before Johnston delivered a decisive thrust.
“The turning point was probably eight and nine,” he said. “I birdied eight by driving it on the front of the green and then I hit a nine-iron to 15 feet on nine and holed the putt for eagle.”