The Morocco international was free on goal but was booked by referee Martin Atkinson when he went to ground as he looked to round Saints goalkeeper Artur Boruc.
It was unclear whether Chamakh was clipped with Holloway not convinced his frontman took the right decision.
"When I was stood on the line I thought the referee had got it wrong," Holloway said.
"Obviously watching it now he didn't. He [Chamakh] went down far too easily for my liking. I can't understand why he didn't chip it or shoot.
"He felt he could take it past the goalie and he felt there was some contact on him but as an away team you are never going to get that are you. He had a great chance to score but he probably didn't make the right choice."
Two goals early in the second half from Dani Osvaldo and Rickie Lambert secured the three points for Saints.
The result leaves Palace with three points from their first six games since returning to the top flight.
"I didn't like the way we capitulated again really," Holloway added.
"We had just let a goal in and it hadn't been a problem until then. We looked much more like a unit and were winning it back much easier than we were last week.
"The lads stuck to what they were doing and unfortunately on a couple of counter-attacks we had chances to maybe even get in front.
"This division is so harsh and so hard. Getting used to it and believing you can play in it can be difficult. We haven't improved quick enough or early enough and we look like we need a goal."
- Sports & Recreation
- Martin Atkinson