The Orica-GreenEDGE sprinter finished ahead of Tanner Putt (United Healthcare) and overall race leader Peter Kennaugh (Sky) after a torrid day of racing.
"It's a different finish to the usual sprints I contest," Ewan said. "I am really happy with the win today, the boys helped me out so much.
"I struggled a little bit over the climbs early on but I had the team around me and they helped me stay as fresh as possible for the final.
"On the final climb I knew (Jack) Bobridge (Trek-Segafredo) and (Peter) Kennaugh (Sky) were strong, they've proven that so I knew couldn't let them get a gap over the top. I fought for dear life and was able to stay with them.
"It's a real confidence boost to be able to win on terrain like this when it's tough."
Kennaugh again benefited from the assistance of team mate Chris Froome - who finished fourth - to cement his lead at the end of the 144km stage from Yarra Glen to Moe.
He leads Froome by 13 seconds while Bobridge moved up to third place on the classification at 31 seconds after initiating the winning move of the day and finishing fifth.
The break of the day was crafted by Chris Harper (State Of Matter/MAAP) and Yuma Koishi (Nippo-Vini Fantini) with the pair building a five minute lead while sharing the spoils of an intermediate sprint and KOM along the way.
After a sustained chase by Avanti Isowhey, Sky and Orica-GreenEDGE, the pair were caught, with Harper resisting the the longest after earlier dropping Koishi.
Shortly after another opportunity to steal the win was taken by Neil Van der Ploeg (Avanti Isowhey), Jason Christie (Kenyan Riders Downunder) and Cameron Bayly (Attaque Team Gusto).
But the trio was given little leeway by a hard charging Sky and Orica-GreenEDGE and were caught with less than 15km to go.
The final climb of the day was decisive with Ewan hanging on as Bobridge, Kennaugh and Jack Haig (Orica-GreenEDGE) made a move 800 metres from the summit before they were joined by Froome and Putt.
It was that selection which decided the result, but with Ewan matching the climbers with each pedal stroke and clearly the fastest in a sprint, the result was a foregone conclusion.
"I gave it one last dig at the end but I knew it was always going to be hard to shake Caleb off,” Kennaugh said. “He stuck to my wheel though, so then I just stuck with him and rode in. I knew I'd dropped Bobridge so thought it was a good chance to get bonus seconds and extend my lead."
— CyclingCentral (@CyclingCentral) February 5, 2016