It was surprising to see them face off early in Obi-Wan Kenobi episode 3 because there was an assumption that the encounter wouldn't happen until the end of Obi-Wan's run. The Jedi Master doesn't want to be the one to kill Anakin because he feels that he is to blame for what happened. There is more significance to Obi-Wan's decision to spare the life of the Sith Lord than the fact that Darth Vader will survive the fight.
Confirmation that the series would see him battling his former Jedi Master as well as Darth Vader came after the announcement that he would return as Darth Vader. Obi-Wan has finally accepted the truth about what happened to his former ally, after realizing that Darth Vader is on the dark path. Obi-Wan solidified his place as one of the greatest Jedi in Star Wars by maintaining his devotion to the Jedi code and refusing to kill an already defeated adversary. The Obi-Wan Kenobi show has established that the Jedi still cares for his former Padawan and remembers him as the great ally he's had for many years. As he told his Padawan, a Jedi's goal is not to take a life but to defend it.
The Jedi Master has a good reason for not killing Darth Vader in Obi-Wan Kenobi episode 6.
Obi-Wan was better equipped to fight Darth Vader in the series finale than in their first fight. This is the reason Obi-Wan didn't kill Anakin in Star Wars: Episode III - Revenge of the Sith. After almost two decades, the actors who played Obi-Wan and Darth Vader return to Star Wars in a Disney+ series. The Jedi master apologized for what happened, but the Sith Lord said his fall to the dark side wasn't his fault.
Obi-Wan's decision to spare his life is an important part of Darth Vader's story. It became clear that a final, more intense rematch was still to come after the Sith Lord defeated the Jedi. After six episodes, the Obi-Wan Kenobi finale will deliver on the promise of a sequel. The Jedi Master is seen by Obi-Wan Kenobi as his lowest point in canon, and he struggles with connecting with the Force because of his flailing faith. His decision not to kill the Sith Lord proves that his principles remain intact even though he has been through a lot. He decided to let his ex-Padawan live after he won the match. He couldn't kill Darth Vader because he continues to associate him with the person he trained as a boy.
Darth Vader's helmet was slashed by Obi-Wan during the fight. As Obi-Wan is overcome with sadness and guilt about what happened to his friend, this stops him in his tracks. Obi-Wan decided to walk away from the fight. In the Obi-Wan Kenobi finale, Lucasfilm delivered that.
The first season of Obi-Wan Kenobi can be watched on Disney+.