The Trotters announced earlier on Monday that they had completed a deal to sign former Nottingham Forest defender Jack Hobbs, but manager Phil Parkinson has also added another player to his attacking ranks.
Magennis makes the switch to the Macron Stadium having netted 20 goals in 81 League One appearances for the Addicks, and the Northern Ireland international has admitted that he is delighted with the move.
The 27-year-old told the club's official website: "It's a massive move for myself and when I found out about the club's initial interest, I was itching to get here.
"I'm absolutely delighted to be a Bolton Wanderers player though and hopefully we can make this season a successful one."
Magennis could feature when Bolton take on West Bromwich Albion in the Championship this weekend.