Alonso received a second yellow card with 25 minutes plus stoppage time remaining in the UEFA Champions League round of 16 first leg, and Guardiola claimed being undermanned made it "very difficult" for his team.
It leaves Bayern with a tricky home leg to navigate on March 11, as a score draw will send Shakhtar into the quarter-finals, although Guardiola is confident.
"We were a man down for a long time and that obviously makes it very difficult. We controlled the play but we created very few scoring chances," the Spaniard told Bayern's website.
"We have to win the return now and we'll do it with our fans behind us."
Guardiola hailed his team's defensive effort in keeping Shakhtar's group of Brazilian midfielders and forwards quiet.
Shakhtar managed just one shot on goal in their temporary home of Lviv.
"We created a few scoring opportunities and made sure that our opponents were unable to create any dangerous situations near our goal," Guardiola said at his post-match media conference.
"We were able to keep Alex Teixeira, Taison and Douglas Costa under control and I am very happy with this."
