The Gunners host the npower Championship side just four days ahead of their showdown with the Bundesliga giants at Emirates Stadium.
It is the start of a crucial period which could well define Arsenal's season, as they go to Tottenham on March 9 and then host Everton before travelling to the Allianz Arena for the second leg.
German centre-back Mertesacker challenged the squad to focus on their first target of not letting Rovers cause another FA Cup upset this weekend.
"We still have an important cup game on Saturday (first) - we absolutely want to advance in the FA Cup, that is why the preparations for Bayern are not that intense yet," Mertesacker said as part of adidas 'football Hangout on air' webchat.
"However, beginning on Sunday the preparations for Tuesday's match will be extreme.
"Bayern are doing superb this year and that is a big challenge for us, but we are looking forward to both legs."
The Germans have not lost since October 28 and have opened up a massive 15-point lead at the top of the Bundesliga, maintaining their ominous form with four straight wins following the winter break.
Former Arsenal and Germany goalkeeper Jens Lehmann believes his old club will face a real challenge to progress further in the competition against last season's beaten Champions League finalists.
Writing in a column for the Sport Bild magazine, Lehmann said: "For an English team it is the worst draw to play a German team directly after the winter break.
"In addition to that Bayern has not been really challenged for once yet in the second half of their season. The only stress they have is the one at the training sessions."
However, Lehmann, 43, believes Arsenal have the players to cause Bayern problems.
He added: "(Bayern coach) Jupp Heynckes will warn his players of the speed that Arsenal still can play in the offensive game, especially Theo Walcott but also more and more Lukas Podolski can be very dangerous.
"Vice-versa, Arsenal will look to stop Bayern creating their good positioning game from which they can accelerate."
Arsenal extended their unbeaten run to five matches with a hard-fought 1-0 Barclays Premier League win at Sunderland.
Gunners boss Arsene Wenger indicated he could rotate his squad for the FA Cup tie, looking to protect the fitness of several key men.
Captain Thomas Vermaelen missed both the last two matches because of an ankle problem, which has been requiring injections.
The Belgian centre-half said during a Q&A with fans on Arsenal's official Twitter account on Thursday: "At the moment I feel great, I trained all week, so hopefully I will be back really quickly."
Wenger later revealed Vermaelen was "looking quite good" and could be included this weekend.
However, the Gunners boss said midfielder Jack Wilshere was still be closely monitored after coming off against Sunderland with a dead leg.
Speaking to the club's official website, www.arsenal.com, Wenger said: "He is having tests today [Thursday] and tomorrow [Friday].
"Jack is looking better. He is still a doubt for Saturday. He's got a kick on the thigh."
Wenger also revealed centre-half Laurent Koscielny remained a doubt with the calf injury which saw him limp out of the warm-up last weekend, after originally picking up the problem while away on international duty with France.
Full-back Carl Jenkinson will be suspended for the cup tie after his red card for two cautions at Sunderland.
With Kieran Gibbs still sidelined by a thigh problem and Andre Santos having joined Brazilian side Gremio on loan, Wenger's defensive options are stretched, so Ignasi Miquel, the 20-year-old Spaniard, looks set to be involved again this weekend.