The Saints were able to increase the lead to 16 at half-time and maintain that lead at the final change.
A one-goal to none final quarter extended the lead to 23 points by the end with the Saints prevailing 10.12 (72) to 7.7 (49).
Brody Webster kicked four for the victors, while skipper Jordan Wolff was named Benalla's best.
For Shepparton, Anthony Andronaco kicked three goals.
Saints coach Jake Pallpratt said the margin probably should have been more, but was pleased with his team's performance.
“It was really good to bounce back with a win on the weekend and start the season 2-1,” he said.
“I thought we had opportunities that we didn’t capitalise on.
“We had a few out on the full and we let ourselves down going forward at times and it could have been a lot different.”
Pallpratt said Webster's four goals were reward for his hard work throughout the day.
“We were happy with the way he competed,” Pallpratt said.
“He nullified a few contests when he was outnumbered and the goals he kicked were reward for his hard work.”
Bears’ coach Ramadan Yze said turnovers cost his team.
“We were pretty good actually,” he said.
“You can't question the effort.
“We had some fumbles and turnovers and red time goals that cost us the win."
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