Lonergan, 32, will play on into a 15th season, playing 186 games since being drafted in 2002.
Cowan, 25, has played 14 games, including nine this year, in seven injury interrupted seasons at the Cats.
“We are really pleased to have both Tom and Josh on board for another year, their football talent, character and the way in which they live our values is an asset to the club,” Geelong general manager of football Steven Hocking said.
“Tom’s football is still of the highest quality and we are confident he will continue to be a leader and mentor to our young defenders in 2017.
“Josh is a young man with resilience and his work ethic and attitude towards his football is why he is so respected within the club.
“When things haven’t fallen his way, Josh’s character has never waivered and we look forward to seeing Josh enjoy continuity in his football.”
Meanwhile Tom Ruggles has been upgraded from the rookie list to the senior list.