The 29-year-old has passed a medical and agreed terms on a three-and-a-half deal after the clubs agreed an undisclosed fee.
The Egyptian centre-half has spent his entire career at Brighton after coming up through the youth ranks, and he has played over 300 games for the Seagulls.
El-Abd signed a new contract last season, but he has fallen down the pecking order under Oscar Garcia this term and has been restricted to 11 appearances in all competitions.
City manager Steve Cotterill said: "Adam is a tough cookie and brings a wealth of experience to the club. Any good back four needs someone like Adam.
"He's capable of playing football from the back and we're delighted to have him here to complement the good defenders already on our books.
"If he's half as popular here as he is at Brighton then that will be great, and I know he will be."
Brighton head coach Garcia insisted the deal would give El-Abd a better chance of playing regular first-team football.
"We wanted to keep Adam in the squad but we understand his position: at his age, he wants to play every game," Garcia said.
"He has been a great player for this club over many years, and I would like to thank him for his hard work since I arrived. We all wish him well for the future because he deserves it."
Brighton chairman Tony Bloom added: "Players of Adam's calibre in terms of loyalty to one club are a rare breed in the modern game. He has given us many years of service having come through the youth set up and has earned his place in our history books.
"He has risen with the club, helping us gain promotion to the Championship via the play-offs in 2004 and as champions in 2011, when he also won the player of the year award, and he has risen to many challenges under a number of different managers.
"I'm sad to see him leave, but he is the type of player who wants to be playing - particularly at this stage of his career. He lives for 90 minutes on the pitch and always gives 100% to the cause. I've no doubt he will prove a fine acquisition for Bristol City.
"He has given excellent service to the club and has been one of our most successful home-grown players. On behalf of all at the club, and all Albion fans, I would like to thank Adam for outstanding service and wish him the very best for the future."
Assuming the deal is ratified by the Football League, El-Abd will go straight into Cotterill's squad for Saturday's home clash against MK Dons.