Boss Brendan Rodgers' "immense pride" at qualifying for the Europa League was tempered by Celtic's 1-0 Champions League defeat by Anderlecht at Parkhead.
The Hoops' 3-0 win in Brussels on match-day two meant the visitors had to equal or better that result in the final Group B game to leapfrog the Scottish champions into third place.
Rodgers' side were out of sorts in the first-half and, despite improvement after the break, an own goal by defender Jozo Simunovic in the 62nd minute meant the Hoops suffered defeat against the Belgian side following losses home and away to Paris St Germain and Bayern Munich.
Rodgers said: "The context of the game affected the performance in the first-half with them having to chase the game. We couldn't keep the ball.
"Midway through the first half we had to change tactically and I was thankful to be in 0-0 at half-time.
"Second half we were better, we were able to stem the flow and be a threat.
"We got the job done but obviously we have a lot of work to do before we can affect that level."
"They were better than us tonight but our aim was to get through to Europa League and come third in the group, that would be a massive achievement and we did that.
"There is immense pride but it is hard to feel that when you have lost.
"We got the job done but obviously we have a lot of work to do before we can affect that level.
"But we are through and we can look forward to it when it comes round in February.
"Maybe some of players felt they have a long way to go before they can call themselves players at this level.
"So we need to be better than we were tonight but we have shown we can be better."
The former Swansea and Liverpool boss moved to dampen down expectations regarding the Europa League.
He said: "We have to have a touch of realism here as well
"There are going to be much better teams than us, we have to be clear on that.
"We have done amazing, we were fourth seeds and not many of them have got into third place.
"We have been able to do that but tonight is an example of a long way to go, and of the gap between the teams at the very top and those just below that."