The Russian held off a gutsy effort from her Romanian opponent, Pavlyuchenkova eventually claiming a 6-4 5-7 6-1 victory in her final match of 2014 at the WTA Premier tournament.
Pavlyuchenkova's triumph sees her become the first Russian to win the Kremlin Cup since Elena Dementieva lifted the trophy in 2007.
The success was not without struggle for the 23-year-old, however, as she had to battle to win a first set that featured just three service holds.
With 31 places separating the two players in the world rankings, most would have expected Pavlyuchenkova to make short work of the world number 61 from that point.
But Begu – competing in her first singles final since September 2012 – battled back superbly to level matters and force a decider in a more disciplined second set from both players.
Yet the 24-year-old, whose 2013 season was severely hampered by a shoulder injury, could not cope with the power of Pavlyuchenkova in the final set.
The Russian, who hit 30 winners in the contest, surged into a 5-0 lead in the third set, and that was a position she did not relinquish, wrapping up her seventh WTA title and her second of the year with a fine backhand passing shot.