BBC Two's BAFTA-nominated series, which began in 2009, is expected to then broadcast its fourth run a year later in 2015.
Armando Iannucci revealed on Twitter last week that the corporation had recommissioned Comedy Vehicle for two series.
British Comedy Award-winning stand-up Lee said in a statement: "I am delighted to be returning to BBC Two, TV's historic home of smart-ass comedy, for two more series, with the same multi-gong-grabbing team as before. I can't really believe this opportunity has been presented to me, and I certainly wasn't expecting it.
"I hope to repay this unprecedented act of blind faith by donning my too-tight jacket to hone another six hours of densely irritating stand-up over the next four years, spliced with aggressive Armando grillings and obtuse filmic codas.
"It will be amazing to be able to move forward and experiment in this unprecedentedly secure position. Thanks to everyone out there who watched the series, wrote about them, or lobbied for their return. I will make you proud. Peace! I'm outta here! You shoulda killed me last year!"
Mark Freeland (Mrs Brown's Boys) has replaced Iannucci as executive producer, while Richard Webb and Tim Kirkby both continue as director and producer.
It is not yet known whether Chris Morris, who acted as script editor for last year's shows, will contribute again.
Watch a clip from Stewart Lee's Comedy Vehicle below: