A first competitive home win for Gordon Strachan's men in World Cup qualifying Group A was decided by a first-half finish from Snodgrass before Naismith made the points safe after the break.
Scotland finished fourth in the group but Everton forward Naismith can see promising signs of improvement under manager Strachan, who replaced Craig Levein in January.
He told Sky Sports: "There's definitely progress being made under the new manager and it was a team performance rather than individuals.
"There were a few comments before about how long it's been since we won a competitive game and we showed that we can do it and can compete against the best.
"We'll take this into the next campaign and show that we can challenge and try and get to a major tournament."
Norwich midfielder Snodgrass, who scored a shock winner in Zagreb back in June, hurt Croatia again before echoing Naismith's comments.
"It's nice," he said. "We're making changes and making progress and the nation should be moving forward.
"I'm delighted with the three points and to get on the score-sheet."