The sports presenter announced the news with fans in a heartfelt Twitter post.
"What a beautiful bunch you all are just confirming Friday will be my last day on @thetodayahow we are going to have a blast for the rest of the week like we have for the last five years it will be nice to unplug the alarm for a while," Gilbert wrote.
The news comes just days after the new line-up for TODAY was announced.
60 Minutes star and journalist Tom Steinfort and TV veteran Deborah Knight will join Georgie Gardner on the panel.
Knight has served as a fill-in and Weekend Today host since joining the network in 2011.
The new line-up was revealed off the back of Karl Stefanovic and Sylvia Jeffreys' shock departure last year.