Yes, this possible with Azure Powershell

Microsoft's documentation has an example for this

$webapp=Get-AzWebApp -ResourceGroupName <group-name> -Name <app-name>

# Set default / path to public subdirectory
$webapp.SiteConfig.VirtualApplications[0].PhysicalPath= "site\wwwroot\public"

# Add a virtual application
$virtualApp = New-Object Microsoft.Azure.Management.WebSites.Models.VirtualApplication
$virtualApp.VirtualPath = "/app2"
$virtualApp.PhysicalPath = "site\wwwroot\app2"
$virtualApp.PreloadEnabled = $false
$webapp.SiteConfig.VirtualApplications.Add($virtualApp)

# Save settings
Set-AzWebApp $webapp