It's a pain but thanks to Jos Lieben I am able to do it with this Powershell function
It's specifically for granting API access on behalf of the Org, but as you can see you can extract the commands to get and use the API token.
Original Author Link: https://www.lieben.nu/liebensraum/2018/04/how-to-grant-oauth2-permissions-to-an-azure-ad-application-using-powershell-unattended-silently/
Function Grant-OAuth2PermissionsToApp{
Param(
[Parameter(Mandatory=$true)]$Username, #global administrator username
[Parameter(Mandatory=$true)]$Password, #global administrator password
[Parameter(Mandatory=$true)]$azureAppId #application ID of the azure application you wish to admin-consent to
)
$secpasswd = ConvertTo-SecureString $Password -AsPlainText -Force
$mycreds = New-Object System.Management.Automation.PSCredential ($Username, $secpasswd)
$res = login-azurermaccount -Credential $mycreds
$context = Get-AzureRmContext
$tenantId = $context.Tenant.Id
$refreshToken = @($context.TokenCache.ReadItems() | where {$_.tenantId -eq $tenantId -and $_.ExpiresOn -gt (Get-Date)})[0].RefreshToken
$body = "grant_type=refresh_token&refresh_token=$($refreshToken)&resource=74658136-14ec-4630-ad9b-26e160ff0fc6"
$apiToken = Invoke-RestMethod "https://login.windows.net/$tenantId/oauth2/token" -Method POST -Body $body -ContentType 'application/x-www-form-urlencoded'
$header = @{
'Authorization' = 'Bearer ' + $apiToken.access_token
'X-Requested-With'= 'XMLHttpRequest'
'x-ms-client-request-id'= [guid]::NewGuid()
'x-ms-correlation-id' = [guid]::NewGuid()
}
$script:url = "https://main.iam.ad.ext.azure.com/api/RegisteredApplications/$azureAppId/Consent?onBehalfOfAll=true"
Invoke-RestMethod -Uri $url -Headers $header -Method POST -ErrorAction Stop
}