While it was a fairly even first half, Cardiff looked more threatening up front and 19-year-old striker Magennis, making his first Championship start, found the underside of the bar with a header, before being forced off with a broken leg.
That all changed on the hour mark when Vennegoor of Hesselink met Marney's corner with a fierce downward header for his first goal since joining the club at the startof September.
Right at the startof the match, Wigan keeper Chris Kirkland very nearly made a disastrous error when he spilled Ledley King's header but he was able to recover and punch the ball away from Michael Dawson, who was poised to nod home.