Swansea were beaten by St Gallen thanks to an 80th-minute goal from Marco Mathys, though they still achieved progress into the next round as Kuban Krasnodar were held at Valencia.
"At the end the most important thing is that we are through," said the Swansea manager after the game.
"How much of an achievement is it for this club? It's not me that you need to ask, but I hope it is huge for Swansea football club.
"We don't know when Swansea will be in Europe again, and I think sometimes we don't appreciate these things when they are happening. I think the same with the cup last year — maybe in three or four years, people will think back and be happy about what we have done."
Swansea now turn their attention back to the Premier League as they face Norwich City on Sunday afternoon.