Pompey had to come from behind, however, as Dave Worrell gave the Devon side the lead after 15 minutes.
The score stayed that wait until shortly after half time when new signing Lomana Lua-Lua equalised.
On as a substitute, Yakubu tormented the Plymouth defense and scored a brace within five minutes (55 & 60), before completing his hat-trick 10 minutes from time.
In between The Yak's second and third goals, Gary O'Neil got on the scoresheet as Portsmouth continued their impressive pre-season form which has seen them defeat Wycombe and Torquay.