We take on the German Bundesliga outfit on Wednesday with a 20:00 (UK) kick-off at the Red Bull Arena.
Both are now back in training and will make the trip for the Group G match.
Bernardo had to come off injured two weeks ago just before half-time in the 3-1 UCL win over Red Star Belgrade.
He's since missed Premier League games against Nottingham Forest and Wolves and the Carabao Cup match at Newcastle United.
Stones hasn’t featured since the Community Shield game with Arsenal back at the start of August.
“Both travel and we are going to decide tomorrow.
“Really happy that they’re back. John couldn’t play one minute this season and Bernardo had a pre-season with the birth of his beautiful daughter and also was injured a little bit, with disruptions, which made it a little bit longer.
“But they’re back which is good news for us.”
Meanwhile, Rodrigo is able to return to the fold for tomorrow night’s clash after sitting out the Newcastle Carabao Cup match and Wolves Premier League game, following his red card against Forest.
The influential midfielder will also miss our away encounter with Arsenal on Sunday but he is available for the Leipzig match.
“Always with negative things you have to take the positives.
“Tomorrow Rodri is going to play the game and then I give him a rest, he will go to Madrid for four or five days before the national team in the international break.”