The closest efforts came midway through the half, with Gary Alexander volleying wide and Dean Keates going close with a low 20-yard free kick.
Brian Laws' side managed to hold on until half time, but not without a few scares. On 26 minutes Damien Delaney shot wide under pressure from a corner.
12 minutes later a mix-up between keeper Tommy Evans and defender Jamie McCombe nearly let Phil Jevons in. The two Scunthorpe players went for the same ball when trying to save a corner, but collided and Jevons pounced on the loose ball. However, Evans got back to make a challenge on the on-loan striker to prevent him getting in a strike on goal.
Shortly before half time City had the visitors on the backfoot again. Stuart Green went through and played it to Gary Alexander. He couldn't get a shot in on goal but pulled it back for Ian Ashbee. The midfielder's first touch was poor and took it away from him when a goal looked on with the goalkeeper off his line.
Scunthorpe came into the game a little more at the start of the second half but City still looked the more likely of the two sides to take the lead.
Phil Jevons headed wide from a good counter attacking move, and was substitued for Stuart Elliott with just under half an hour to go, and the Northern Irish international looked threatening.
Elliott was booked 2 minutes later for an inocuous challenge on Lee Featherstone. Andy Dawson couldn't get his free kick past the City wall for Scunny's best chance of the game.
They were made to pay for wasting that opportunity when City took the lead with just 5 minutes to go. Elliott played the ball down the channel to Delaney, and he got the better of Featherstone to pull the ball back. Michael Branch found himself unmarked, and took one touch before blasting the ball past Evans to make it 1-0.
Gary Alexander made the win safe in the 90th minute with a similar chance, and none of the 11,885 crowd in Boothferry Park would deny that City fully deserved the 2-0 win.
City line-up (4-4-2): Musselwhite; Regan, Whittle, Anderson, Delaney; Green, Ashbee, Keates, Williams (Branch 78); Alexander, Jevons (Elliott 63).
Un-used subs: Deeney, Burton, Peat.