The 30-year-old spent six years at Carrow Road after moving to Norfolk in 2004 from Tottenham Hotspur.
Addicks boss Phil Parkinson told the club website: "He's an experienced centre-back with great quality and I'm delighted he's agreed to join us."
He added: "Of all the centre-backs out there in the summer he was the one I targeted. It's taken a while to do the deal for various reasons.
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"When I spoke to him I said I want him to push on again in his career. He's a good age for a centre-half and hopefully he's got many years left in him, starting with the next two seasons here at Charlton."
Doherty, who was born in County Donegal, started his career at Luton in 1997, where he played in defence and as a striker.
Two years later he moved to White Hart Lane and settled into the central defensive role.
After appearing as a youth international, he won his first full Republic of Ireland cap in 2000 against Greece.
He moved to Norwich after four and a half seasons with Spurs and was voted the club's player of the season in 2005/6.
Source: BBC Sport
Source: BBC Sport