The Australian goalkeeper produced a brilliant save to deny Mikel Arteta from the penalty spot in the fourth minute of added time to allow the Cottagers to force a 3-3 draw in an enthralling contest in North London.
As they did midweek against Schalke, Arsenal skipped away to a two-goal lead through summer signings Olivier Giroud and Lukas Podolski before Fulham's newest star Dimitar Berbatov got them back on level terms with a goal of his own and then an assist for Alex Kacaniklic before the break.
Berbatov then edged the visitors in front with a 67th minute penalty but Giroud was able to join him on two match goals with another header two minutes later.
It was after that when controversy struck with referee Phil Dowd wrongly calling Sascha Riether for handball in the area but justice was served as Schwarzer came up with the goods to deny Arteta low to his left.
The opener came in the 11th minute when Theo Walcott's outswinging corner was met by Giroud who powered a near post header from the edge of the six-yard box into the palms of Schwarzer who could only parry it into the roof of the net. It was the Frenchman's first Premier League goal at home for the Gunners.
Just over ten minutes later, the home side were two to the good when they took full advantage of the fact Fulham had a gap down the left side following Kieran Richardson's hamstring injury with Arteta running on to a through ball before delaying his cut-back from deep in the area for Podolski to prod home from close range.
Fulham picked up their output almost immediately and replied when Berbatov somehow found himself unmarked inside the six-yard box to easily nod home Bryan Ruiz's inswinging corner just before the half-hour mark.
Five minutes prior to the break, the Bulgarian ace turned provider when he clipped a dangerous ball into the area from the right side for substitute Kacaniklic to hit a well-placed bouncing header from 15 yards which evaded Vito Mannone.
Disaster struck for Arsenal in the 67th minute when Arteta was pick-pocketed by Ruiz before the Spaniard pulled down the Costa Rican in the area with Dowd having no hesitations in pointing to the spot. Berbatov stepped up and coolly slotted to Mannone's right to give Fulham the lead.
But it was short-lived as Giroud again rose above the pack to meet Walcott's rightwing cross to head home his third Premier League goal.
Schwarzer had made a couple of decent saves in the second half to deny Giroud's swerving left-footer from range as well as cutting off Santi Cazorla's dangerous effort but none were as good as his magnificent stop at the death to give Martin Jol's men their 16th point of the campaign, which has them equal with Arsene Wenger's seventh-placed side who would be disappointed by today's result.
Emirates Stadium, London - 60,093