His superb goal in the first half set them on course for a fifth win of the season, which would also extend their unprecedented unbeaten start to eight games.
And he scored a second after the break, although Bremen remained in the match until the end after Serge Gnabry responded immediately afterwards.
But former Bremen striker David Selke scored a third at the very end to move Leipzig in second in the table and maintain their fine record-breaking form.
Two changes for Leipzig but Bremen unchanged
No debuting club had gone seven games unbeaten at the start of its first Bundesliga season until Leipzig’s 1-0 victory against VfL Wolfsburg, the result that cost the Wolves’ head coach Dieter Hecking his job.
They made two changes from that game, with captain Dominik Kaiser replacing the injured Marcel Sabitzer, and Keïta coming back in for Stefan Ilsanker.
Werder Bremen were unbeaten in the previous three games, with just one defeat since Alexander Nouri took charge of the team. They returned from the international break last weekend with an impressive 2-1 win against Bayer Leverkusen. The same team that started that match began here.
Keïta magic after Leipzig struggle to break down Bremen
Yussuf Poulsen had a great early chances for the hosts. He was found by Kaiser, before using his strength to force his way into the box, only to be denied by Felix Wiedwald.
However the first half offered few clear chances for either side. Leipzig had more of the ball, but showed their frustration when they were without it, with three of their four midfielders going into book for fouls on Bremen players.
Bremen could also have had a penalty. An excellent ball from Gnabry set up Ousman Manneh. Péter Gulácsi came out to get the ball, perhaps getting the slightest of touches on it but also bringing down the young striker. It would have been a very soft spot kick to give though.
But before the break came the moment of magic from Keïta to put his side in front. He beat Manneh with ball, dribbled his way through two pairs of defenders, rounded Wielwald and finished sublimely. A truly wonderful individual goal from the 21-year-old Guinean.
Gnabry and Forsberg go close
Bremen had a couple of real chances to draw level early in the after the break. Gnabry almost had a shot set up by Theodor Gebre Selassie, however a vital late challenge form Bernardo denied him.
From the following corner Bernardo headed on to his own post, Gnabry had a shot blocked, and Bremen appealed for a penalty from a resulting handball. The only trouble was that the former Arsenal man was actually the guilty party.
Again the game remained competitive, but Leipzig’s first real chance, other than Willi Orban heading over a couple of corners, came when Emil Forsberg had a long range effort saved by Wielwald. Poulsen then headed the rebound goalwards, with Wiedwald tipping it over to make sure it wasn’t going in.
Selke comes back to haunt his former side
Leipzig’s first substation was to bring on the former Bremen striker Selke, and he made an almost immediate impact. Keïta started and finished the move, finding Poulsen who flicked on to Selke, with Keïta getting his second by heading in the following cross.
Almost straight from the kick-off though, Bremen responded. Manneh brought the ball forward, found Fin Bartels, who crossed to Gnabry to slide in at the far post.
It was set up a grandstand finish, with both sides going full tilt in the final ten minutes. The closest Bremen came was when Gnabry was given offside after a slight touch from Aron Jóhannsson on the ball through from Manneh.
Leipzig though had the momentum in the closing stages, however Bremen were then awarded a free-kick, taken on the left. Wiedwald had come forward, but Leipzig quickly won back the ball and surged forward on the counter, with Selke outrunning the keeper and slotting it gently in from the edge of the box with the final touch of the game.