Ayew, 31, returned from a hamstring injury to score in Sunday's 2-2 draw at Reading, which secured their place in the playoffs.
But Cooper said the Ghana international had suffered a "slight setback."
"It's nothing too serious and he won't be in doubt for the play-off games," Cooper told BBC Radio Wales Sport.
"There are a few others who have been nursing overuse injuries and wear and tear if you like - there just hasn't been any let up. It's been heavy.
"Don't get me wrong, we're not working for the NHS or digging up roads, It's not the worst life in the world but in our domain, it's been a really, really heavy schedule.
"And that's why I think the players deserve a lot of credit. We haven't got the biggest squad and we've been light in some positions throughout the season but we haven't let it affect us.
"We have a way of working we believe in it, we don't change particularly when things are not going well and we believe that will get us to where we want to be.
"We're still on course I guess and hopefully we can get the last bit right."
Swansea face relegation-haunted Derby County at the Liberty Stadium on Saturday before they end the regular season at already promoted Watford on 8 May.
"We still want to win the next two games," Cooper added.
"The league position that you finish in will have an effect on your play-offs because our league is so unpredictable and I said at the weekend that if you assume you get the opposite.
"But we want to use the remainder of the domestic campaign and the lead into the play-off games as a productive period and be the best we can be." Read Full Story