Amir wrapped up the home side's innings after they resumed at the overnight position of 278 for nine, bowling last man Shannon Gabriel to finish with six for 44, an effort which improved on his previous best of six for 84 against England at Lord's in 2010.
That occasion was, ironically, to prove his undoing for the then teenaged fast bowler's role in the spot-fixing scandal that overtook the game and resulted in him being banned from the game for five years.
Play had started 90 minutes later than scheduled due to the continuing effects of heavy, torrential rain on a damp outfield which reduced play to just 55 minutes on the second day.
Pakistan started their reply brightly with Azhar Ali looking ominous before he chased a wide delivery from Alzarri Joseph to give a catch to wicketkeeper Shane Dowrich tumbling in front of first slip.
Ahmed Shehzad, playing his first Test for almost two years, also opened brightly with a flurry of shots, including five boundaries in 31 only to be trapped leg-before on the back foot by Holder.