The Metcalfe sisters played for Wales together for the first time when lock Branwen came off the bench for her first cap against Canada at the 2025 World Cup.
They started the uncapped fixture against the Baa-Baas but join forces in the XV for the first time at Test level against Japan.
Branwen, 20, starts her sixth successive Test and has a new second-row partner in fellow bright prospect Aiono.
Nel, 21, returns on the wing rather than full-back for her first cap since the World Cup after a knee injury that forced her to sit out the Six Nations.
“She was a shining light at the World Cup, which was tough for us,” said Lynn.
“Every time that she gets the ball, something will happen. She has got fitter, stronger and faster, and she’s excited to go out there on Saturday.”
Wales are 11th in World Rugby’s rankings, a spot above Japan.
Last month the Sakura Fifteen lost 55-21 to Italy and were beaten twice by Ireland, 31-24 in the WXV Global Series and 43-19 in an extra Test.
“Japan ran Ireland close in the first Test and they are very efficient in what they do, very regimented,” said Lynn, who opts for six forwards on his bench.
“They’ve got a very good maul and we are not going to be taking them lightly at all.”