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As the question basically says, is there a way to stop permissions inheritance on a list or a library via PowerShell?

Moreover there is a way to change user or group permissions on this list/library?

Thanks a lot!

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Since SharePoint 2013/Online supports a sets of APIs, CSOM or REST APIs could be consumed in PowerShell for that purpose.

How to stop permissions inheritance for a List in SharePoint Online

Prerequisites: SharePoint Online Client Components SDK

The example below shows how to assign unique permissions for a list using CSOM API in PowerShell:

[System.Reflection.Assembly]::LoadWithPartialName("Microsoft.SharePoint.Client")
[System.Reflection.Assembly]::LoadWithPartialName("Microsoft.SharePoint.Client.Runtime")


Function Get-ClientContext([string]$Url,[string]$UserName,[string]$Password)
{
    $SecurePassword = $Password | ConvertTo-SecureString -AsPlainText -Force
    $context = New-Object Microsoft.SharePoint.Client.ClientContext($Url)
    $context.Credentials = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($UserName, $SecurePassword)
    return $context
}


Function List-BreakInheritance([Microsoft.SharePoint.Client.ClientContext]$Context,[string]$ListTitle)
{
    $list = $Context.Web.Lists.GetByTitle($ListTitle)
    $list.BreakRoleInheritance($true, $false)
    $Context.ExecuteQuery()
}


$UserName = "jdoe@contoso.onmicrosoft.com"
$Password = Read-Host -Prompt "Enter the password"    
$Url = "https://contoso.sharepoint.com/"

$context = Get-ClientContext -Url $Url -UserName $UserName -Password $Password
List-BreakInheritance -Context $context -ListTitle "Tasks"
$context.Dispose()

As an alternative, you could also consider to utilize REST API.

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Unfortunately this can't be done with PowerShell (yet). You have to use Office 365 API for this action.

Ref: Index of Windows PowerShell for SharePoint Online cmdlets

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