The Portuguese winger had looked the most likely to create danger throughout a tepid first period as his free-kick came crashing back off the post.
However, he made no mistake when presented with a chance by a poor pass from Jesus Gamez after the break, turning Martin Demichelis before rocketing a shot high past Willy Caballero 12 minutes into the second-half.
Malaga were way off the excellent form they had displayed just before the winter break throughout and offered little in reply with Roque Santa Cruz's near-post header which flashed wide the closest they came to an equaliser.
Victory means Depor remain in the relegation zone only on goal difference, whilst Malaga stay in fourth but are now level on points with Betis and just one ahead of Levante.
Paciencia was only appointed on Monday as the Depor board finally lost patience with Jose Luis Oltra after a run of eight games in all competitions without a win.
As is often the case, the home players reacted to the change in the best possible manner.
Deportivo could have been three goals ahead in the opening half an hour as Caballero nearly turned Bruno Gama's shot into the path of Riki before Gama wasted another clear opening and Pizzi's free-kick struck the base of the post.
Joaquin then wasted a great opportunity to give Malaga an undeserved half-time lead as he fired straight into the body of Daniel Aranzubia when presented with a clear sight of goal.
However, it was the hosts who were back on the front foot at the start of the second-half as Riki somehow fired wide with the goal at his mercy just six minutes after the restart.
Pizzi though showed is strike partner how to do it just six minutes later as he latched onto Gamez's mishit pass before accelerating past Demichelis and firing a powerful shot in off the inside of Caballero's near hand post.
Manuel Pellegrini responded by introducing Javier Saviola and Diego Buonanotte but the Argentinean pair could do little to liven a flat Malaga performance as Deportivo comfortably held on for only their third league win of the campaign.