With 32 minutes gone, and the score 0-0, Smith fell to the ground under the challenge of Sofiane Boufal.
But, rather than point to the spot, Moss showed Smith his fifth yellow card of the season, which means he will be suspended for one game.
“For the ref to book me doesn’t help because that’s my fifth yellow card of the season,” said Smith. “I spoke to him after and he apologised and said it was a penalty.
“I don’t mind him admitting it but the fact he booked me and can’t get it rescinded means I’ll miss the next game.”
Manager Eddie Howe said: “I can’t work out what the referee has seen, but that’s football, you live and die by those decisions and I think he’s got it wrong.”
Bournemouth took the lead just before the break when Scotland winger Ryan Fraser slotted a first-time effort past Fraser Forster.
But the Cherries, seeking their first win over the Saints since March 2016, were pegged back when Southampton striker Charlie Austin swept home the equaliser just after the hour mark.
England winger Nathan Redmond provided the pass for the striker to score after coming on as a half-time substitute.
The point takes Southampton up to 11th in the Premier League, while Bournemouth move above Newcastle into 14th.
Howe’s men have league games against Manchester United, Liverpool and Manchester City coming up in what appears a tough run of matches.