Werner and Kai Havertz, the marquee signings of a free-spending transfer window for Chelsea, were each named in a front three for the visit to the Amex Stadium.
The former was key in breaking the deadlock, which Jorginho did in the 23rd minute after Werner was brought down by Mat Ryan.
Lucas Trossard briefly restored parity but a spectacular strike from James and a fortuitous one by Zouma sealed maximum points for Frank Lampard's men.
Neither goalkeeper was troubled in the first 20 minutes before Brighton gifted Chelsea the opening goal with some careless play in their own half.
Steven Alzate conceded possession and Jorginho pounced with a well-weighted throughball to Werner, who was felled by the outstretched knee of the onrushing Ryan.
Craig Pawson showed no hesitation in pointing to the spot and Jorginho tucked away the penalty with his trademark hop on the run up as he sent Ryan the wrong way.
Alzate went closest to producing a response when his drive drew a diving stop from Kepa Arrizabalaga before Ryan had to be alert to prevent Werner beating him at his near post.
Nine minutes after the second-half restart, Brighton were level with a goal that will raise more questions about Kepa's place in the team.
The Chelsea goalkeeper allowed Trossard's effort from outside the box to sneak under his hand and into the bottom-left corner, but parity lasted just 99 seconds.
Ryan was left with no chance as James fired a ferocious long-range effort into the top-right corner, and he was similarly helpless 10 minutes later when Zouma's tame effort deflected in off Adam Webster.
Those goals were separated by Lewis Dunk spurning a great chance to equalise, however, there was little threat from Brighton after Chelsea's third.
What does it mean: Fortune smiles on Frank
Brighton had more possession and more shots on goal than Chelsea, whose win came with a degree of fortune.
It was not the kind of dominant display some may have expected given their recent spending, with Chelsea grateful for a penalty and a large deflection in a win that means they are still unbeaten in league competition against Brighton and join Manchester United and Arsenal in becoming the third team to amass 2,000 Premier League points.
Jorginho spot on
Midfielder Jorginho continues to be clinical from 12 yards. He has scored all eight of the penalties he has taken for Chelsea in all competitions (excluding a costly miss in the 2019 EFL Cup final shoot-out against Manchester City), including five in the Premier League.
19 - Since he joined Chelsea in 2018, Kepa Arrizabalaga has conceded more Premier League goals from outside the box (19) than any other goalkeeper. Weakness. pic.twitter.com/3NA1WgpYmC— OptaJoe (@OptaJoe) September 14, 2020
Kepa will have been disappointed not to keep out Trossard's effort and, with Edouard Mendy's arrival from Rennes reportedly imminent, the writing appears to be on the wall. The Spain international has conceded more Premier League goals from outside the box (19) than any other goalkeeper since joining Chelsea in 2018.
Key Opta stats
- Brighton have won just one of their 10 home Premier League games in 2020 (D4 L5), the fewest of any side to have played two or more home matches in the competition this calendar year.
- Since the start of last season, Chelsea’s 20 away Premier League games have produced 81 goals (42 for, 39 against), at least 14 more than any other side on their travels.
- Chelsea have scored each of their past 16 penalties in the Premier League since Eden Hazard missed from the spot against Man City in April 2017.
- Trossard has scored three goals in his past six Premier League games for Brighton, as many as he netted in his first 26 appearances in the competition before this.
- Zouma scored his second Premier League goal for Chelsea on his 72nd appearance and his first since September 2015 against Arsenal.