Key defender Keeffe, 23, was contracted for next year but AFL.com.au understands he has re-signed for another season, with out-of-contract midfielders Thomas, 21, and Dwyer, 26, re-signing for two more years.
Keeffe, 204cm, is the most experienced of the trio, having made his debut in 2011, with Thomas and Dwyer among seven Magpies who have debuted this year. Ruckman Brodie Grundy will become the eighth when he plays against Greater Western Sydney on Saturday.
Keeffe joined the Magpies in the 2009 rookie draft and played five games in his debut season.
He looked to have cemented a spot in the Magpies' back six when he played the first nine games of 2012, but he ruptured his right anterior cruciate ligament in round nine against Adelaide and underwent a knee reconstruction.
That injury and a bruised kidney he suffered in his first match back for Collingwood's VFL team in late May meant Keeffe did not return to the Magpies' senior team until last round against Gold Coast.
Keeffe looms a vital player for the Pies in coming seasons, when his ability to hold down a key defensive post would give Collingwood greater flexibility to use Ben Reid as a swingman.
Thomas joined Collingwood via pick No. 75 in the 2009 draft after the Broadbeach local rejected the chance to join Gold Coast as a zone player.
Thomas' early days at Collingwood were dogged by injury, with foot stress fractures limiting his appearances in the VFL during the past two seasons.
But the 176cm inside midfielder made his debut in round one this season against North Melbourne and has now played 12 games, including the last seven straight.
Thomas has averaged 19.4 disposals and nearly four clearances a game this season and AFL.com.au understands he attracted the interest of several opposition clubs before re-signing.
Dwyer is the latest mature-age recruit to become an instant hit in the AFL despite being overlooked in draft after draft.
After being snared by the Magpies in last year's rookie draft, the former Port Melbourne star was elevated from the Pies' rookie list ahead of round one and debuted alongside Thomas against the Roos.
The midfielder/forward quickly found his feet at the game's highest level and, apart from missing rounds 10 and 11 with a groin injury, has become a fixture in the Magpies' team, averaging 18.4 possessions and one goal a game.
Nick Bowen is a reporter with AFL Media. Follow him on Twitter @AFL_Nick