An entertaining series had tilted this way and that to leave the sides locked at 3-3 heading into the finale at Lahore, but Malan's 78 not out set the table for a decisive result in England's favour.
Malan came to the party at the perfect time after a low-key series, sharing an unbeaten 108-run stand with Harry Brook to push the total up to an imposing 209 for three.
Pakistan's pursuit was undone inside two overs, with star batters Babar Azam and Mohammad Rizwan producing a rare double failure, and they limped to an underwhelming 142 for eight.
England decided not to risk captain Jos Buttler or pace bowler Mark Wood, both preserved for the World Cup later this month, but Woakes' return to fitness stepped up a notch as he claimed three wickets for 26 runs.
The visitors lost the toss but made the running as their openers racked up 35 off the first three overs. Phil Salt picked up exactly where he left off in a match-winning effort last time out, crashing three of his first six deliveries to the ropes.
Alex Hales was also lively, collecting three consecutive fours off the uninspired Mohammad Wasim and picking gaps at deep third, mid-wicket and cover, before Pakistan dragged things back in the fifth over, taking out both men in the space of three balls.
Hales was trapped plumb in front of middle as Mohammad Hasnain jagged a delivery off the seam but Salt fell foul of a sloppy run out as new man Malan ball-watched at the striker's end.
The number three would go on to make amends for his part, starting with a well-paced stand of 62 alongside the inventive Ben Duckett. The pair started carefully but began unlocking their boundary options and took a major liking to Shadab Khan's mixed bag of leg-breaks and variations. They took 20 off his second over, Malan launching the first of his three sixes over deep midwicket and Duckett hitting one straight over the bowler's head.
Duckett was cut off in full flow by an opportunistic piece of glovework from Rizwan, who turned a deflection off the inside edge into a sharp run out. But Malan found another willing partner in Brook, who chipped in 46 not out in the unbroken century stand. Babar played an unintentional role in their success, dropping Malan at cover on 29 and Brook on 24 off a particularly simple up-and-down chance off the unlucky Haris Rauf.
Brook had needed just four balls to find his six-hitting range of Shadab and repeated the feat three more times during his stay, while England ended on a high with 20 off Wasim's final over.
Pakistan's entire game plan hinges on their exceptional opening partnership, but with everything on the line England dismissed them both inside two overs.
Babar was first to go, suckered in by Woakes' slower ball and chipping straight to Brook. That cranked up the pressure on Rizwan but he was sent packing when Reece Topley's second ball zipped past the bat and into off stump.
That exposed a middle order that has been shielded for too long by the top two's consistency and David Willey soon had Iftikhar caught behind. A powerplay total of 37 for three effectively ended the home side's hopes and the rest of the innings played out tamely as the required rate soared to implausible heights.
Shan Masood made 56 as the game drifted, eventually falling to Woakes before the all-rounder added a third success in the last over of the tour.