With the visitors 1-0 ahead at St James' Park on Sunday, Cisse floored Seamus Coleman in the Everton box - only to receive no reprimand.
Insult was then added to injury as Cisse levelled proceedings, after which goals from Ayoze Perez and Jack Colback put Newcastle 3-1 ahead.
Kevin Mirallas struck late on to set up a tense finale, yet the home side held on - much to Martinez's dismay.
Speaking about the Cisse incident, the Everton boss told Sky Sports: "It is unacceptable to see an action like that go unpunished. It was a clear elbow to try to hurt someone.
"I don't think those are actions we want to see. The referee should have seen it."
The loss was a third in a row for Everton, who will end 2014 sitting 12th in the table.
Martinez added: "It's concerning because we're not in a good moment with suspensions and injuries.
"It seems everything that could have gone against us has. You don't want that to creep in and create negative momentum.
"It's one of those moments where the momentum is not with us. We need to make sure you work a little bit more in a clever manner and make sure we keep clean sheets.
"We need to just get a win that gets us going the right way again. It's a real important moment to redirect our season."