The Trotters looked in control of the contest at all times and frankly seemed more comfortable with the final occasion compared to their Devon counterparts, with goals from Kyle Dempsey and Dion Charles putting Bolton into a two-goal lead at half time.
The Pilgrims failed to make any improvements after the break, and strikes from Elias Kachunga and Gethin Jones put the destination of the trophy beyond doubt after just 60 minutes.
Bolton started the better of the sides in the Wembley sunshine and took advantage from a set-piece situation to leave the Argyle faithful in silence after just four minutes.
Welshman Declan John swung in an inviting left-footed delivery from a corner which found Dempsey, who had peeled off at the back post - his looping-headed effort across goal left Plymouth keeper Callum Burton rooted.
Wanderers were catching Steven Schumacher's men countless times on the break and doubled their lead in the Wembley contest just six minutes later, with Kachunga and Dempsey linking up before slotting in Charles, who fired in Bolton's second.
The Northern Ireland international netted his 19th goal of a prolific campaign with that convincing finish, just over a week after the forward bagged his first goals for his national side in a 2-0 success over San Marino.
Despite sitting second in League One, Plymouth were visibly struggling to deal with the occasion early on in the contest, with goalscorer Dempsey bursting through on goal with little resistance - Burton was able to save a relatively tame effort from the 26-year-old to prevent a 30-minute Argyle implosion.
The Pilgrims did start to grow into the game after 25 minutes and had their first notable opportunity of the match in the latter stages of the first half - Danny Mayor found marksmen Ryan Hardie with a low cross, but James Trafford managed to keep the striker's effort out.
Ex-Sheffield Wednesday man Mayor was arguably lucky to remain on the pitch when his poorly-timed tackle on Josh Sheehan was only punished with a yellow card - any type of review on that decision may have seen Plymouth's comeback become even more implausible.
Ian Evatt's side continued their relentless pressing after the half-time break and were rewarded handsomely, with Charles harassing the Plymouth backline into a poor clearance, which left Kachunga streaking in on goal.
The 30-year-old took an assured touch away from his Pilgrim counterpart and unleashed an efficient finish past the diving Burton, sending the large Bolton contingent at Wembley into delirium.
It took just over an hour for Wanderers to extend their lead to four, with Jones getting the better of Plymouth's Hardie from a corner kick - cue sections of the Green Army making their way to the exits.
Plymouth will want to put a Wembley horror show swiftly behind them and secure promotion to the Championship, with a humbling trip to the Mazuma Stadium to face Morecambe awaiting the Pilgrims on Good Friday.
Bolton are embroiled in a hotly-contested battle to earn a playoff berth in the closing stages of the third-tier campaign - Evatt's men travel to Devon to clash with Exeter City on Friday afternoon.