Malaysia sped ahead in the first half scoring a goal but Pakistan caught up and subsequently won after scoring three consecutive goals.
Abdul Hassim Khan scored two goals for team green while skipper Mohammad Imran scored one.
Pakistan's recent victory, however, does not qualify them for the International Hockey Federation (FIH) World Cup next year.
The team had gotten off to a good start in the Asia event but Thursday's defeat against South Korea had kept them from clinching the series.
The four-time World Cup champions had entered the Asia Cup desperately needing the title to book their place for the 2014 global tournament in The Hague, Netherlands.
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Cricket has gone downhill and pear shaped. Now hockey. What next? I'll keep it to myself.
Will this be a wake up call, OR not?