The Italian driver soared to the top of the one-make Renault Clio Rally5 series timesheets when early leader Paulo Soria dropped over two minutes on SS3 with a deflated front right tyre.
Cogni remained unchallenged from that moment onwards and gradually built up a 23.2sec advantage over Spaniard Sergio Fuentes, who holds second place overnight.
Patrik Herczig trailed Fuentes by almost one minute to end fourth overall, while Soria chalked up a handful of stage wins to haul himself back up the order.