Georginio Wijnaldum's late goal proved decisive as the Eredivisie leaders earned the point they needed to secure second spot in Group E in a game that was spread over two days following heavy rain in Portugal.
Estoril led 3-2 at half-time on Thursday when a downpour called proceedings to a halt, with the teams returning to complete the match on Friday.
Strikes from Memphis Depay and Luciano Narsingh sandwiched Toze's effort to cap an eventful opening and leave the visitors 2-1 ahead after 14 minutes.
But Kuca levelled matters on the half-hour mark and Diogo Amado's goal gave Estoril hope of a vital triumph.
It was Wijnaldum who had the last say, though, his cool 82nd-minute finish ending the hosts' qualification hopes with a game still to go.
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