D'Jaffo, signed in midweek after being released by Aberdeen in January, twisted to head in Liam Lawrence's 69th minute corner to clinch only Mansfield's second win in six games and complete a remarkable double over City.
The goal came seconds after Mansfield midfielder Lee Williamson had lobbed over an empty net. Central defender Rhys Day also had a late header cleared off the line.
But for the rest of the match Hull dominated. Ben Burgess rattled the bar with a deflected second half drive and substitute Jamie Forrester almost rescued a point, but his late pile driver struck Tony Vaughan and was scrambled clear.
The Tigers had rung the changes in a bid to find a first goal in three games, Ian Ashee, Jason Price and Andy Holt all coming back into the midfield. The Stags, also on a poor run of just four points from five games, gave a home debut to D'Jaffo whose last game was in the African Nations Cup for Benin.
The striker's physical presence upset the City defence in the opening minutes but when he got his chance to score he flicked Wayne Corden's cross well wide.
The only other clear chance of a scrappy start fell to Mansfield striker Iyseden Christie who turned and shot straight at keeper Boaz Myhill in the 17th minute.
Three minutes later, Corden's attempted back pass was almost intercepted by Jonathan Walters as Hull began to dominate the midfield and then Burgess skied over.
Mansfield, now forced to play on the breakaway, twice went close on the half hour. First Craig Disley's 25-yard speculative shot was easily saved and then D'Jaffo's close range header from a pinpoint Lawrence cross was held by the diving Myhill.
City almost grabbed the lead deep into first half injury time when Walters raced clear on to Junior Lewis' incisive pass before Day slid in with a last ditch tackle.
Five minutes into the second half, Day again came to Mansfield's rescue - just doing enough to force Burgess to shoot tamely at the keeper from six yards.
As Hull's pressure increased Burgess' deflected 20 yard drive rattled the bar, but Mansfield hung on.