Deng, with one Socceroos cap, recently captained the Olyroos as they secured qualification for the Tokyo Olympics.
The 22-year-old will depart for the as-yet unnamed club in Japan after playing at Victory since 2015 – including a loan stint at Dutch club Jong PSV in 2016/17 – where he won an FFA Cup and an A-League championship.
“The club has given me so much over the journey, and as tough as it is to say goodbye, I think it’s a great reflection of Victory’s professionalism and investment in their players,” Deng said.
“It was a tough decision to make but, for my professional career, the opportunity to play in the J1 League is one I couldn’t pass up.”
Victory football operations manager Paul Trimboli said the club would look to the current transfer window – which closes on January 31 – to bring in another defender.
“On behalf of everyone at the club we wish Tommy all the best for the next phase of his football career, he is always welcome at Melbourne Victory,” Trimboli said.
“With only a couple of days left in the transfer window, we’re working hard to find a suitable replacement to fill the spot made available in our squad.”
With Tim Hoogland on the comeback trail from injury, James Donachie and the inexperienced Ben Carrigan are now the only true centre-backs at Victory’s disposal.
Versatile defender Leigh Broxham will be suspended for this week’s A-League clash with Perth Glory after he received two yellow cards against Sydney FC.
Victory play Kashima Antlers in their AFC Champions League play-off match on Tuesday night, then Perth Glory away in the A-League on Saturday night.