The Gunners got away with a largely average display at the Constant Vanden Stock Stadium, where a second-half header from Andy Najar looked to have put the Belgians on course for a famous win to ruin manager Arsene Wenger's 65th birthday.
However, just as they did in rescuing a point at home to Hull with a stoppage-time equaliser in the Barclays Premier League on Saturday, Arsenal struck late as first left-back Kieran Gibbs volleyed in a superb finish in the 89th minute and then substitute Lukas Podolski crashed in a dramatic winner.
Arsenal now have qualification for the knock-out stages back in their own hands ahead of next month's return tie against Anderlecht at the Emirates Stadium, and then hosting Group D leaders Borussia Dortmund.
Mertesacker, though, knows the Gunners cannot afford the continued inconsistencies which have seen early-season promise quickly turn back to familiar questions about the direction of Wenger's squad following only five wins from the opening 14 matches.
"Everyone knows that it was a difficult start for us and our confidence is not that much how we wanted it," the German defender said.
"The character is good, the mentality is good, but football-wise, we lack a few things.
"Our passing game is not as efficient as last year
We are not at our best
We have to admit that, be honest with ourselves and train harder."
By his own admission, Mertesacker has not produced the consistent form of last season, with the 6ft 7in German culpable for failing to deal with a cross which lead to Hull taking the lead on Saturday.
The 30-year-old retired from international football after Germany's summer World Cup triumph but accepts the highs in Brazil came at some cost to his subsequent club performances.
"Personally it is difficult at the moment because that was really a long season last year and to come back from that World Cup and get the motivation back..
I am nearly back, but you can feel there is something missing at the moment," he said.
"With those games, the belief and the mentality is there, but the motivation will come back.
"We didn't even have time to celebrate [the World Cup win] properly, that was the first thing, but you realise month after month what happened.
"I am still not there [taking in] what happened in Brazil, maybe in five or 10 years you can really realise what was going on there.
"We came back to Berlin, got on the stage, waved our hands, showed the World Cup and then everyone disappeared to their families to get some holidays, some rest and calm."
Mertesacker said it was a struggle to relax into "a proper holiday" and said the resumption of club football was on his mind.
"That was really a problem, but I am happy not to have picked up an injury yet and I am confident that I have already been through the dangerous period," he added
"I am really happy that I am slowly fit and ready for the proper fight during the winter period."
Wenger allowed his World Cup winners to miss the opening games of the season to fit in a suitable break.
"It is harder mentally because we started literally when the season (had already) started
I have never experienced that," Mertesacker said
"But slowly, now it is 100 days or so after the World Cup final, so the season is going to start (for real)."
Source : PA
Source: PA