Thousands of fans applauded the two-and-a-half minute long film which ran as the concert got underway with nearly an hour's delay, the Polish PAP news agency reported.
Warsaw city hall requested the singer air the clip in the wake of an online petition against her concert by a group of young Catholics furious it would coincide with the Polish capital's annual World War II commemoration of the doomed uprising against the city's Nazi's occupiers.
As of Wednesday, the petition had gathered 54,000 supporters for the "Material Girl's" concert to be called off out of respect for the estimated 200,000 people who died in the 63-day uprising by Polish partisans.
Nazi German dictator Adolf Hitler ordered the deportation of the half-a-million residents who survived before his forces systematically bombarded the city leaving it as little more than a smouldering heap of rubble.
"August 1 is a day of remembrance in Poland. We pay our respects to those who survived and those who perished in the uprising. We won't allow the desecration of our hallowed symbols," reads the Internet petition launched by a group calling itself the Youth Crusade.
Warsaw ground to a halt Wednesday at 5 pm (1500 GMT) and sirens wailed as residents stood still to observe the annual minute's silence across the capital remembering the loss of life in the largest single rebellion against Nazi Germany during WWII.
The Youth Crusade also slammed the 53-year-old Queen of Pop's on-stage antics as "attacking the Catholic faith... offending Jesus Christ by burning crosses and wearing a crown of thorns" as well as promoting homosexuality and pornography.
Warsaw Archbishop Henryk Hoser urged residents to pray against what he termed Madonna's "blasphemous concert". Poland remains one of Europe's most devoutly Roman Catholic countries.
Madonna's ongoing "MDNA" world tour has been been marked with her trademark brand of controversy.
The pop diva outraged fans in France who had paid more than 250 euros (300 dollars) per ticket by quitting the stage in Paris after barely 45 minutes on July 26.
France's far right National Front has taken legal action against her for screening a video showing its leader Marine Le Pen with a swastika on her forehead during an earlier concert in Paris.
The video was also shown at a Tel Aviv gig in May kicking off the tour, covering about 30 countries and wrapping up in Australia in 2013. (AFP)
