The Irish No 1 looked in trouble when he crashed to five-over par after just six holes at Royal Adelaide.
After a three over par 75 in the first round, the Esker Hills man got off to a bad start in round two with bogeys at the fourth and fifth and a double bogey at the sixth.
But he bounced back with a birdie-eagle burst on the 14th and 15th to card a one-over par 74 that helped him make the seven-over par cut with three shots to spare.
Lowry is ten shots behind pace-setters Michael Foster, Matthew Griffin and Josh Younger with Paul Culter the best of the Irish on two over after a 77.
But there was disappointment as Co Louth’s Simon Ward and Royal Dublin’s Niall Kearney missed out by a shot after rounds of 80 and 79.
Former Irish Boys International Andrew Lynch, who has been living in Australia since last December, also missed the cut after an 80.
Kearney will be hoping to bounce back on home turf in next month’s AIB Irish Amateur Open at Royal Dublin.
The May 9-11 event has attracted 91 overseas players from 17 countries, including 35 from France.