Niasse was not in Koeman's plans at the start of the season and had not featured under the current Toffees manager until last week, when he scored as a substitute against Sunderland in the EFL Cup.
And with Everton continuing to struggle in the Premier League on Saturday - trailing Bournemouth after a run of three straight defeats - Niasse was called from the bench again to net a brace and win the game.
The former Hull City loanee is not now available for the European meeting with Apollon Limassol at Goodison Park on Friday (AEST), but Koeman stands by the decision he made at the time, adding that the squad will look better when other attacking players return.
"We had to make that decision a long time ago," the manager told a pre-match news conference. "At that time, [Niasse's] situation was not the situation it is now.
"In life, you don't get a second chance and you have to decide. The decision was made also [due to] other players, who are not available. Maybe in several weeks, yes, [they will be back] and you make your decision."
On the importance of their home group games, Koeman added: "You have to win the three at home and then you have an opportunity to go through to the next round."
Defender Mason Holgate says the Everton team are feeling confident again, although he insists there was never any doubt that they would recover from a poor run.
"We had a difficult start to the season but, as a team, we never worried that we wouldn't get back together," he said.