England and City skipper Houghton was making her first competitive start since January and looked fit and strong on her return to action from an Achilles injury.
Houghton’s return will be a major boost for City ahead of the 2022/23 campaign.
Gareth Taylor utilised a mixture of experienced and younger players throughout the game.
City got off to the perfect start when Millie Pullen tapped home from a couple of yards out after the Durham keeper palmed a low shot into her path.
MacIver then made a good save on 16 minutes as Durham worked their way into the game.
The visitors levelled early in the second period following a set-piece routine, but City were soon back in front when the impressive Fowler lashed a low left-foot shot home from the edge of the box.
And there was even better to come as Laura Coombs struck a sublime long-range shot into the top left corner from 20 yards five minutes later.
It was all City by that point and Pullen then scored her second two minutes after with another tap-in from close range as the visitors began to wilt.
City went into the final 25 minutes of the contest leading 4-1, with Taylor bringing on the majority of his development squad for much needed experience.
Khiara Keating, on the day her first professional contract was announced, made an excellent save with her feet and was the busier of the two keepers in the time that remained.
Durham pulled one back late on following a corner on the right, but a young City side held on to see out the game comfortably.
Starting XI: MacIver, Ramsden, Taylor, Houghton, Prior, Coombs, Fowler, Dahou, Samson, Raso, Pullen