Joseph, 20, was due to make his first Saxons appearance but the London Irish centre has been forced to drop out of the side due to a groin injury.
Waldouck, who will make his seventh appearance for England's second string, is one eight changes to the Saxons team that beat the Ireland Wolfhounds 23-17 last week.
"It's nothing serious and he (Joseph) could play with it but it might not be in his best interests," said Saxons coach Jon Callard.
"He's got a bright future but as he's just come back from a different injury we didn't want to compound his problems.
"We always planned to make changes over the course of these two games and it means there are more chances for those who've been playing well in the Aviva Premiership and in Europe this season."
Bath full-back Nick Abendanon replaces Delon Armitage, who has been suspended following his arrest on suspicion of assault, and Northampton's Ryan Lamb takes over from Freddie Burns at fly-half.
Waldouck will partner Leicester's Billy Twelvetrees in midfield while Gloucester's Jonny May starts on the wing in place of Matt Banahan.
In the pack, Leicester lock Ed Slater makes his first Saxons start in place of Matt Garvey.
Gloucester prop Nick Wood and Harlequins hooker Chris Brooker get starts in the front row and Exeter's Tom Johnson takes over from Thomas Waldrom at number eight.
England Saxons team to play Scotland A at Galashiels on Friday, February 3 (kick-off 7.30pm): N Abendanon (Bath Rugby); U Monye (Harlequins), D Waldouck (London Wasps), B Twelvetrees (Leicester Tigers), J May (Gloucester Rugby); R Lamb (Northampton Saints), B Spencer (Saracens), N Wood (Gloucester Rugby), C Brooker (Harlequins), P Doran-Jones (Northampton Saints), E Slater (Leicester Tigers), G Robson (Harlequins), J Gaskell (Sale Sharks, capt), A Saull (Saracens), T Johnson (Exeter).
Replacements: J Gray (Harlequins), R Harden (Gloucester Rugby), K Myall (Sale Sharks), D Seymour (Sale Sharks), P Hodgson (London Irish), F Burns (Gloucester Rugby), M Benjamin (Worcester Warriors).
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