Charlton had thrashed Rovers 5-1 at the Memorial Stadium in November and they were convincing victors again, although they had to do it the hard way after a mistake by Patrick Bauer gifted Rovers a 12th-minute lead.
The Addicks defender slipped while attempting a back pass, enabling Jermaine Easter to burst clear on goal and round Dillon Phillips before slotting into an empty net.
Magennis' free-kick hit the crossbar, while Adam Chicksen's cross was tipped behind by Will Puddy via the woodwork as Charlton sought an equaliser before the break.
Parity was restored four minutes before the interval with Magennis heading home from Joe Aribo's free-kick.
And the duo combined in almost identical circumstances five minutes into the second half, an unmarked Magennis again using his head to convert from Aribo's set-piece delivery.
Aribo turned provider once again just after the hour, playing a low ball across the face of goal which was swept in from close range by Jorge Teixeira to make it 3-1.
Magennis completed his treble after 73 minutes, latching on to Andrew Crofts' pass and then firing an angled shot beyond Puddy in some style.
Report supplied by the Press Association.
Match ends, Charlton Athletic 4, Bristol Rovers 1.
Second Half ends, Charlton Athletic 4, Bristol Rovers 1.
Attempt missed. Matty Taylor (Bristol Rovers) header from the centre of the box is close, but misses to the left.
Foul by Morgan Fox (Charlton Athletic).
Lee Brown (Bristol Rovers) wins a free kick in the attacking half.
Jorge Teixeira (Charlton Athletic) wins a free kick on the left wing.
Foul by Matty Taylor (Bristol Rovers).
Attempt saved. Ellis Harrison (Bristol Rovers) header from the centre of the box is saved in the top centre of the goal.
Foul by Fredrik Ulvestad (Charlton Athletic).
Lee Mansell (Bristol Rovers) wins a free kick in the attacking half.
Substitution, Charlton Athletic. Nicky Ajose replaces Chris Solly.
Substitution, Charlton Athletic. Kevin Foley replaces Ezri Konsa Ngoyo.
Attempt missed. Josh Magennis (Charlton Athletic) header from a difficult angle on the left is close, but misses to the left.
Attempt saved. Peter Hartley (Bristol Rovers) right footed shot from the centre of the box is saved in the top centre of the goal.
Chris Solly (Charlton Athletic) is shown the yellow card for a bad foul.
Matty Taylor (Bristol Rovers) wins a free kick in the defensive half.
Foul by Chris Solly (Charlton Athletic).
Corner,  Charlton Athletic. Conceded by Peter Hartley.
Adam Chicksen (Charlton Athletic) wins a free kick on the right wing.
Foul by Lee Mansell (Bristol Rovers).
Substitution, Charlton Athletic. Fredrik Ulvestad replaces Joe Aribo.
Attempt missed. Matty Taylor (Bristol Rovers) left footed shot from outside the box misses to the right.
Adam Chicksen (Charlton Athletic) is shown the yellow card.
Foul by Adam Chicksen (Charlton Athletic).
Stuart Sinclair (Bristol Rovers) wins a free kick in the defensive half.
Goal!  Charlton Athletic 4, Bristol Rovers 1. Josh Magennis (Charlton Athletic) right footed shot from the centre of the box to the top right corner. Assisted by Jorge Teixeira.
Corner,  Bristol Rovers. Conceded by Patrick Bauer.
Attempt saved. Liam Lawrence (Bristol Rovers) right footed shot from the centre of the box is saved in the top centre of the goal.
Foul by Josh Magennis (Charlton Athletic).
Tom Lockyer (Bristol Rovers) wins a free kick on the left wing.
Corner,  Charlton Athletic. Conceded by Stuart Sinclair.
Byron Moore (Bristol Rovers) is shown the yellow card.
Corner,  Charlton Athletic. Conceded by Peter Hartley.
Corner,  Charlton Athletic. Conceded by Tom Lockyer.
Substitution, Bristol Rovers. James Clarke replaces Daniel Leadbitter because of an injury.
Corner,  Charlton Athletic. Conceded by Liam Lawrence.
Ezri Konsa Ngoyo (Charlton Athletic) wins a free kick in the defensive half.
Foul by Liam Lawrence (Bristol Rovers).
Goal!  Charlton Athletic 3, Bristol Rovers 1. Jorge Teixeira (Charlton Athletic) left footed shot from very close range to the centre of the goal. Assisted by Joe Aribo following a set piece situation.
Delay over. They are ready to continue.
Josh Magennis struck a hat-trick as Charlton came from behind to brush aside Bristol Rovers at The Valley.