Schneider will be handed the captain's arm-band, usually worn by Chelsea midfielder Michael Ballack, who is injured, for Saturday's Group D qualifying match.
With Ballack's fellow midfield play-maker Tim Borowski also injured, Schneider, 32, has the added responsibility of organising the attack as well as captaining Germany for the first time on his 77th appearance for his country.
"Bernd will be running the midfield and will organise the attack," said national assistant coach Dieter Flick.
Having smashed San Marino 13-0 last September, Germany are expected to run up a cricket score but the German camp are doing their best to talk down any prospects of a big win.
"We are ignoring the previous win over San Marino, we are just concerned with picking up a win," said Flick.
Werder Bremen striker Miroslav Klose, the top goal-scorer at last year's World Cup, is expected to partner Schalke 04 striker Kevin Kuranyi up front.
As well as Ballack, who had an ankle operation last April, and Borowski, striker Lukas Podolski, midfielder Bastian Schweinsteiger and forward Oliver Neuville are all missing with injuries.
Germany, who play Slovakia in Hamburg on June 6, top Group D with 13 points from the Czech Republic and Republic of Ireland, but with at least a game in hand over their rivals.