The 22-year-old striker, making his home debut after joining on loan from Everton, bagged his first career hat-trick as Palace got back to winning ways after four straight defeats.
Pompey did at least manage to hit their second league goal of the season, courtesy of some comical Palace defending which let in new signing Dave Kitson to cancel out Vaughan's opener.
But Vaughan struck twice more in the second half and Neil Danns added a penalty to leave Pompey, who remain in administration, still searching for their first win.
Palace, of course, only recently came out of administration themselves, and the storm clouds which have been following these two clubs around appropriately opened moments after the teams kicked-off.
But Vaughan's spirits were not dampened by the downpour and he struck in the 14th minute after Owen Garvan played a one-two with Danns before bursting into the Pompey penalty area.
His square pass was slightly behind Vaughan but in a flash the striker swivelled and lashed his shot past Ashdown and into the top corner.
However, Pompey were gifted the equaliser thanks to a dreadful mix-up in the Palace defence.
Goalkeeper Julian Speroni came charging out to collect a long clearance but Anthony Gardner clearly did not see or hear him coming and nodded the ball over the Argentinian, allowing Kitson to fire into an empty net.
Ashdown denied Palace a second with a superb save to tip Garvan's dipping 20-yard drive over the top before Kieron Djilali cut inside and curled a fine effort onto the inside of the post.
Pompey started the second half brightly and David Nugent's strike was ruled out by an offside flag before Hayden Mullins, playing against the club where he started his career, shot too close to Speroni.
But nine minutes into the second half Vaughan raced onto Alex Marrow's pass over the top, got to the ball just before Ashdown and expertly lifted it over the keeper and into the net.
Vaughan completed his hat-trick four minutes later after Danns nodded Paddy McCarthy's cross into his path.
And nine minutes from time, Danns was felled by Michael Brown and, having waved away Vaughan's attempts to take the spot-kick, smashed the ball past Ashdown for the fourth.