After seven minutes Michael McIndoe found Dele Adebola, who finished calmly with a left-foot shot from 18 yards.
City pressurised but Wade Small wasted a good Owls chance when he mis-hit from close range. City keeper Adriano Basso then smartly denied Sean McAllister.
Bradley Orr made it 2-0 when he fired from Adebola's pass before Lee Bullen grabbed an injury time goal.
Bristol City boss Gary Johnson:
"There was a decent atmosphere in the ground and Dele Adebola scored the type of goal we brought him in for early on to give everyone a boost.
"We had enough chances to have won 5-2 but I was delighted with the lads because they worked hard throughout and we got our football back together after a bad result."
Sheffield Wednesday manager Brian Laws:
"The second goal killed us off after we had begun the second half brightly. We don't look as though we have three goals in us at the moment and the players know that.
"I'm trying to bring in another striker but it isn't easy. For one thing, not every player wants to join a club in our position, facing a real battle. We have some home games to come and need to capitalise on them."
Bristol City: Basso, Orr, Carey, McCombe, McAllister, Sproule, Johnson, Elliott (Skuse 88), McIndoe, Carle (Trundle 71), Adebola (Byfield 58).
Subs Not Used: Weale, Fontaine.
Goals: Adebola 7, Orr 56.
Sheff Wed: Grant, Bullen, Hinds (Wood 85), Beevers, Gilbert, Small, Kavanagh, Bolder, O'Brien (McAllister 46), Tudgay (Boden 82), Burton.
Subs Not Used: Burch, Wallwork.
Booked: Gilbert.
Goal: Bullen 90.
Att: 15,520
Ref: Rob Shoebridge (Derbyshire).
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