Santon played the full 90 minutes for his first appearance following a knee injury, and is now expected to be on the substitutes' bench when Newcastle travel to Wolves at the weekend.
Newcastle were three up after 22 minutes through goals from Michael Richardson, Shane Ferguson and Dan Gosling.
But a brace from Stephen Dobbie, following a goal from Luke Moore, enabled Swansea to level within two minutes of the interval.
Newcastle reclaimed the lead when troubled Toon striker Nile Ranger converted from the penalty spot after he was fouled in the box, and the scoring was completed when Greg McDermott converted from close range after Sammy Ameobi's shot was saved.
NEWCASTLE UNITED: Elliot, Henderson, Santon, Abeid, Dummett, Kadar, Sammy Ameobi (Moyo 84), Richardson, Ranger, Gosling (Inman 81), Ferguson