The Pilgrims eased into half-time 2-0 up after man-of-the-match Peter Halmosi scored a goal and laid on one for French midfielder Nadjim Abdou.
However, Hull sent on Dean Windass at the break and the veteran striker netted twice, either side of what turned out to be the match-winner from the Pilgrims' leading scorer Sylvan Ebanks-Blake.
Argyle made four changes for the all-Championship clash - a dress-rehearsal of the league encounter between the two sides - while Hull manager Phil Brown went even further and brought in seven players.
Hungary international Halmosi engineered Argyle's opening two goals, which came inside three minutes. His free-kick struck defender Damien Delaney and fell for Abdou, who poked the ball past goalkeeper Boaz Myhill.
Another free-kick from the same position, almost immediately afterwards, then curled straight in after Dutch defender Marcel Seip had distracted Myhill.
Recalled Argyle goalkeeper Luke McCormick made a crucial double save just before half-time to deny Stuart Elliott and Hull captain Nicky Barmby, and then spectacularly turned aside a shot from Delaney early in the second period.
Windass pulled one back after a long ball forward was flicked on by Barmby into the path of the 38-year-old, who chipped the ball past McCormick.
Argyle extended their lead when Ebanks-Blake broke down the left and squared the ball for Halmosi, who played it straight back for the 13-goal striker to lash the ball home.
Hull responded immediately when Windass curled in a 35-yard free-kick after Seip had been penalised for fouling Caleb Folan.
Pilgrims substitute Lukas Jutkiewicz, the on-loan Everton striker, nearly put the issue beyond doubt when he ran directly at the Hull defence and fired in a shot that beat Myhill but rebounded off the post.