Greek debutant Tsitsipas will face six-time champion Federer while Zverev will face Austrian Dominic Thiem.
Nadal briefly kept alive his qualification hopes in Friday's first match at the O2, valiantly battling back from a set down to beat the already qualified Tsitsipas.
That would leave Zverev, Nadal and Tsitispas with identical 2-1 records.
Nadal lifts the ATP World No 1 trophy following the presentation on Saturday.
"Nobody expected (Nadal) to be out from our group".
Rafael Nadal staged another comeback to stay in contention for a semifinal spot at the ATP Finals.
He finished that match with five unforced errors - including two double-faults - but had 26 in this match.
Zverev converted his first match point with an ace.
Reaching the final is another milestone in a breakthrough season after he also beat Federer on the way to the Australian Open semifinals. He'll come up against Thiem, who impressed by beating those same two players in the group phase this week.
"I've got to keep on playing at the level like I have this year, and then I will create some chances", he said.
And unfortunately for him, defending champion Zverev was on fine form.
Federer also spoke about how it feels to have a huge fanbase: "It's fun, it's an absolute privilege to be so well liked around the world when it comes to the tennis support that I get".
"It's OK, my body feels well now, " Tsitsipas said. I don't feel pain anywhere. I feel fresh, honestly.
I felt from the get-go I had good rhythm off the baseline and on the serve and that I felt like he was living dangerously if he was not going to play great tennis. "So I don't have any problem with that".
Federer wasted three break points when Tsitsipas served at 4-2 then lost out in a marathon 13-minute ninth game as Tsitsipas served for the first set.
After the match, Nadal was presented with a trophy on court for having secured the year-end No. 1 ranking.
It's the fifth time that the 19-time grand slam victor ends the year atop the rankings, tied for second on the all-time list with Djokovic, Federer and Jimmy Connors.
The three greats are alongside Jimmy Connors on that tally, while only Pete Sampras (six) has achieved it more often.
"After all the things I went through in my career in terms of injuries, I never thought at the age of 33 and a half I would have this trophy in my hands again".
At 21, Tsitsipas is the youngest of the four semi-finalists but, although this is his first time in the ATP Finals, he is arguably playing better than anybody else in the tournament.