The day after mechanical problems put him out of contention in the series opener, Ewan finished several lengths clear of his rivals on Geelong's Ritchie Boulevard circuit.
The win put Ewan fourth in the series standings, eight points behind Austrian Marco Haller (Katusha-Alpecin).
Barring a disaster, Haller should win the series after Thursday's third and final race at suburban Williamstown.
Haller finished third on Wednesday behind Australian star Heinrich Haussler (Bahrain-Merida).
It is the 24-year-old's first win at his new team Lotto-Soudal.
Ewan has much bigger fish to fry, but Wednesday's win is symbolic for the sprint ace.
The Lexus Blackburn Bay Crits continue Thursday 3 January with live coverage on the Cycling Central Facebook page from 1pm AEDT.
Last year was tumultuous, with Ewan a last-minute scratching from the Mitchelton-Scott team for the Tour de France.
It would have been Ewan's Tour debut and once he missed out on a start, he was always going to leave the Australian team.
"It's a lot of change obviously this year ... it's probably the biggest change in my career so far," Ewan said.
"Last year was disappointing for me, so I really wanted to get this year off to a good start.
"In the scheme of things, the Bay Crits is a small race, but it's so important to get that winning feeling back and hopefully it can continue on from here."
Ewan also brought Roger Kluge with him to Lotto-Soudal from Mitchelton-Scott and the German leadout specialist starred on Wednesday, shredding the field with his work at the front of the race.
Kluge was not feeling at his best on Wednesday morning and nearly did not race.
"I forced him to start - I think he surprised himself," Ewan said.
Ewan even made his own attack midway through the race.
The day after Ewan's mechanical dramas put him out of contention, this time it was the turn of sprint rival Brenton Jones (Delko–Marseille Provence KTM) to have bad luck.
Jones dropped his chain on the second-last lap and did not contest the final sprint.