The Spaniard saw the Bundesliga champions return to top form with Saturday's 8-0 hammering of Hamburg, claiming his side are now "back in the groove" following a sluggish return after the winter break.
Arjen Robben and Thomas Muller both grabbed braces at the Allianz Arena to help set Bayern up for their return to European action.
The Ukrainian champions have not beaten Bundesliga opposition at home in the Champions League since 1980, and Philipp Lahm knows his side "have to make the next round".
"Bayern’s minimum target is always the quarter-finals," he added after the draw for the last 16 was made.
Guardiola could see Xabi Alonso (hamstring) join Lahm (ankle), Javi Martinez (knee) and Thiago Alcantara (knee) on the sidelines but still has plenty of strength in his squad.
The cause for Mircea Lucescu's hosts will also likely be made all the more tricky by the fact that they have not played a competitive fixture since December's 1-1 draw with Porto.
Shakhtar - without suspended midfielder Taras Stepanenko - do not get their domestic title defence back under way until later this month but Luiz Adriano, the Champions League's leading goalscorer this season with nine, is confident there will be no signs of rustiness from his team-mates.
"[Bayern] are still in a different rhythm of the game. Bayern play matches every three to four days, whereas we played several friendly matches during a month-and-half," the Brazilian told the club's official website.
"However, they were not easy and for us it is also a good training session. I can say that the team are now in excellent physical condition.
"We have a few more training sessions left before the game. I think we can come fully prepared to face Bayern."
Bayern have not found Ukraine a happy hunting ground in recent years, with just one win, one draw and three defeats from their visits to the country.
Lucescu's side have also been given backing by former player Henrikh Mkhitaryan to cause an upset.
He has witnessed first-hand the quality that Bayern have at their disposal, and the Borussia Dortmund playmaker feels his former club have the capabilities to take a positive result into the second leg in Munich on March 11.
"Every game starts at 0-0. I’m sure that Mircea Lucescu’s team have every chance to beat Bayern," he told his former club's website.
"Shakhtar are a great team with decent players. If the Pitmen play the way they are capable of, Bayern will have a lot of problems."
