Tinkler's Hunter Sports Group (HSG) licence to own the club has been revoked by Football Federation Australia, who will own and control the Jets' new licence.
Thompson is understood to have been involved in talks with both Tinkler and the FFA about buying the Jets.
Tinkler said on Wednesday that Dundee were offering A$5 million ($5.4 million) for the club and a deal was imminent.
But the FFA's decision to strip Tinkler of the ownership licence sidelines him from any sale.
"HSG has behaved in a deplorable way towards the players and staff of the club in failing to meet basic obligations to pay wages," FFA chief David Gallop said in a statement.
Gallop said the FFA would continue talks with several parties.
The FFA moved on Newcastle after Tinkler earlier placed the club into voluntary administration with debts of A$2.7 million.
The on-field woes were compounded when Tinkler sacked seven players in January, further riling the FFA, who were already upset at club finances.
Tinkler purchased the Jets' licence in 2010, and a year later assumed ownership of the Newcastle Knights rugby league club.
In June last year, the NRL took back control of the Newcastle Knights from Tinkler after he failed to get a multi-million dollar bank guarantee.
- AAP
