Driving the No. 1 Porsche car for the second and final stints of the six-hour race, Webber finished third in his last competitive race before retirement.
As he took to the track, the Australian admitted that the moment did start to get to him.
"For the final stint it was pretty emotional putting my helmet on for the last time," he said
. "I enjoyed the last stint and I got the chance to bring the car to the checkered flag for the top three finish, and this was the maximum we could get today.
"It has been such an incredible three years for me with Porsche, together with Timo (Bernhard), Brendon (Hartley) and the whole team. Nothing is forever, I'm stopping at a good time and I'm looking forward to seeing everybody again soon."
Having already claimed the manufacturers' title earlier in the series, Porsche also claimed the drivers' championship when its No. 2 car -- driven by the trio of Romain Dumas, Marc Lieb and Neel Jani -- finished sixth in on Saturday. Webber's No. 1 car was fourth in the overall standings.
Webber's F1 career
Webber spent 14 seasons in F1 before switching to the long-distance series in 2014. He won nine races and stood on the podium 42 times in 215 F1 starts, finishing third in the drivers' championship on three occasions.
He will be remembered as a gutsy driver who was involved in two of F1's more spectacular moments of recent times. His thrilling overtaking maneuver on rival and friend Fernando Alonso at Eau Rouge during the 2011 Belgium Grand Prix exemplified his racing spirit.
He was also involved in one of the sport's most frightening crashes -- his Red Bull car taking off and somersaulting after running into the back of Heikki Kovalainen's Lotus at Valencia in 2010. Webber emerged shaken, but, remarkably, unscathed.
After leaving F1, the Australian quickly found success in the World Endurance Championship, winning the 2015 title for Porsche in only his second season.
"Since I made my announcement we've had quite a bit of success, winning quite a few races with Porsche," Webber told CNN World Sport prior to the Bahrain race, pointing to WEC victories in the US and China.
"There's been great, great memories, but I think that's a good sign because I want to remember it like that. As time goes on, you know it's totally the right decision."