Bartusiak's header gave Frankfurt a deserved lead at the break, after forcing several good chances in the first half.
Bayern fought back in the second but the woodwork and Veronica Boquete's disallowed goal meant they fell to defeat.
Bartusiak heads home the opener
It was a slow start to proceedings in Munich, though both teams were trying to attack. Melanie Leupolz had an early shot blocked by the Frankfurt defence, but it was the visitors who would hit the target first. A free-kick was only cleared as far as the edge of the area and Laura Störzel, who forced a fine save from Tinja-Riikka Korpela.
The wings were providing the early openings for Frankfurt, who began much better than Bayern. Nora Holstad was extremely busy early on and dealt with any threats well, though plenty of corners were conceded as a result. Kerstin Garefrekes felt she could have done better after Korpela spilled a header, only to fire straight at the Finn.
The only action for Anne-Kathrine Kremer in the first 25 minutes came from a hopeful cross from the right, which she did well to punch clear. Any momentum Bayern were building would be soon quashed, as Frankfurt took the lead on the half-hour mark. A corner was powerfully met by Saskia Bartusiak, whose header found the top corner.
It could have been even better for Matt Ross' side before the break, only to see Mandy Islacker's looping volley hit the roof of the net. Veronica Boquete had the champions' only attempt on target during the only first half, though her effort was tame and easily held by Kremer - ensuring her side led going into the break.
Bayern battle back but can't find a crucial equaliser
The second half began similarly to the first, with the pitch becoming increasingly slick as rain continued to fall. Getting the ball out wide and trying to force an opening from the wings was the order of the day, though it rarely paid dividends. The closest either came was when Garefekes' cross was scrambled away at the back post.
Frankfurt fans had reason to be concerned when Islacker and Melanie Behringer both went for a 50/50 ball. Thankfully for Frankfurt, she was able to continue after treatment. Moments later, Vivanne Miedema looked to have provided the inspiration for a comeback off the bench, though Boquete was flagged for offside - much to her dismay.
Bayern were finally beginning to force the issue, though injury concerns took over for Frankfurt as Dzsenifer Marozsán limped off in severe pain and it looks unlikely that she'll be fit for their crucial UEFA Women's Champions League clashes against VfL Wolfsburg.
Miedema then crashed a header off the bar in the final stages, with their pressure beginning to tell on the tiring legs of the opponents. Mana Iwabuchi couldn't convert an excellent cross to the back post from Gina Lewandowski, and that proved to be the final chance of the match. It was a vital win for Frankfurt, who remained a point behind Wolfsburg. Bayern's title party has been put on hold, though it should just be a matter of time before they are crowned champions.