After sometime digging into the .net Sharepoint client sdk, I found how SharepointOnlineCredential class does it, thus allowing access to Sharepoint SOAP Services.
So, as said already by Fei Xue, the Azure AD token is not valid to access Sharepoint SOAP services (althoug the token is valid to allows access to REST services...). To access Sharepoint Online services, you will need to use some sort of claims authentication, either by requesting user consent or by directly using a known user and password.
As we can't use the .net SDK in our php app, we have investigated how the SDK creates the requests to get authenticated when using user credentials directly:
First send your authentication credentials as a SAML-WSSecurity POST request to the authentication endpoint https://login.microsoftonline.com/rst2.srf:
POST https://login.microsoftonline.com/rst2.srf
Content-Type: application/soap+xml; charset=utf-8
Content-Length: [calculate]
Host: login.microsoftonline.com
<?xml version="1.0" encoding="UTF-8"?>
<S:Envelope xmlns:S="http://www.w3.org/2003/05/soap-envelope" xmlns:wsse="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-secext-1.0.xsd" xmlns:wsp="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" xmlns:wsa="http://www.w3.org/2005/08/addressing" xmlns:wst="http://schemas.xmlsoap.org/ws/2005/02/trust">
<S:Header>
<wsa:Action S:mustUnderstand="1">http://schemas.xmlsoap.org/ws/2005/02/trust/RST/Issue</wsa:Action>
<wsa:To S:mustUnderstand="1">https://login.microsoftonline.com/rst2.srf</wsa:To>
<ps:AuthInfo xmlns:ps="http://schemas.microsoft.com/LiveID/SoapServices/v1" Id="PPAuthInfo">
<ps:BinaryVersion>5</ps:BinaryVersion>
<ps:HostingApp>Managed IDCRL</ps:HostingApp>
</ps:AuthInfo>
<wsse:Security>
<wsse:UsernameToken wsu:Id="user">
<wsse:Username>[user]</wsse:Username>
<wsse:Password>[password]</wsse:Password>
</wsse:UsernameToken>
</wsse:Security>
</S:Header>
<S:Body>
<wst:RequestSecurityToken xmlns:wst="http://schemas.xmlsoap.org/ws/2005/02/trust" Id="RST0">
<wst:RequestType>http://schemas.xmlsoap.org/ws/2005/02/trust/Issue</wst:RequestType>
<wsp:AppliesTo>
<wsa:EndpointReference>
<wsa:Address>sharepoint.com</wsa:Address>
</wsa:EndpointReference>
</wsp:AppliesTo>
<wsp:PolicyReference URI="MBI"></wsp:PolicyReference>
</wst:RequestSecurityToken>
</S:Body>
</S:Envelope>
The response, in xml format, will come with the security token in it:
....
<wst:RequestedSecurityToken>
<wsse:BinarySecurityToken Id="Compact0">t=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&p=
</wsse:BinarySecurityToken>
</wst:RequestedSecurityToken>
...
Then using the security token extracted from the previous response, you need to send a GET request to your tenant credentials endpoint: https://yourtenantname.sharepoint.com/_vti_bin/idcrl.svc/
You will need to send an Authorization header with the format: BPOSIDCRL + space + token. Like:
GET https://yourtenantname/_vti_bin/idcrl.svc/
Host: yourtenant.sharepoint.com
Authorization: BPOSIDCRL t=EwA4A06hBwAUNfDkMme61kIdXqvj9tWnUbHtXWEAAREB5clgLb8J/VvxRFIKLUnd9SRyoBHmTHFk0viit2FMlGXak5NJKJhicT8MiZmgA2HoTrJM1EgXCNUpmWqrX1LQRNfs0PHEV4XncjI9lnphsSTiFSCDjmdCKtW4TmV8n18xJHvBtDUWdvCT2lBti8
The response to this request will set a cookie that we need to capture and use in our next requests to the soap services:
Set-Cookie: SPOIDCRL=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; path=/; secure; HttpOnly
Finally by attaching this cookie to every request to Sharepoint Services we get authenticated responses:
POST https://yourtenantname.sharepoint.com/_vti_bin/Lists.asmx HTTP/1.1
Host: yourtenantname.sharepoint.com
Content-Type: application/soap+xml; charset=utf-8
Content-Length: [calculate]
Cookie: SPOIDCRL=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; path=/; secure; HttpOnly
<?xml version="1.0" encoding="utf-8"?>
<soap12:Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap12="http://www.w3.org/2003/05/soap-envelope">
<soap12:Body>
<GetListCollection xmlns="http://schemas.microsoft.com/sharepoint/soap/" />
</soap12:Body>
</soap12:Envelope>