Toshack and the 29-year-old full-back were involved in a public falling-out ahead of Wales' final two World Cup qualifiers last month over the player's fitness and availability when Thatcher claimed that Toshack accused him of being "scared".
He said at the time: "I won't be spoken to like that, the manager has questioned my commitment and credibility in public. He said I was scared of reprisals following the clash in Cardiff last October when I was [sent off] for the incident with Polish midfielder Kamil Kosowski."
Thatcher, 30 at the end of this month, now joins Robbie Savage in international isolation as far as Toshack is concerned.
Toshack will also be without his captain Ryan Giggs and Everton's Simon Davies in Cyprus, but Craig Bellamy and Robert Page both return after injury. Giggs is still recovering from a broken jaw, suffered in Manchester United's Champions' League home draw with Lille last month, and has missed his club's past five games.
Davies damaged a hamstring in Everton's 1-0 win over Middlesbrough on Sunday and manager David Moyes immediately informed Wales that the midfielder would not be available. Cardiff's Martyn Margetson has been named as the third goalkeeper. With Gillingham's Jason Brown still out with a hand injury, Ipswich's Lewis Price is expected to make his debut.
Wales squad (friendly v Cyprus, Limassol, 16 November: P Jones (Wolves), Margetson (Cardiff), Price (Ipswich), D Collins (Sunderland), J Collins (West Ham), Delaney (Aston Villa), Duffy (Coventry), Edwards (Wolves), Gabbidon (West Ham), Page (Coventry), Partridge (Bristol City), Ricketts (Swansea), G Roberts (Tranmere), Fletcher (West Ham), Koumas (Cardiff), Robinson (Sunderland), Vaughan (Crewe), Williams (West Ham), Bellamy (Blackburn), Earnshaw (West Bromwich Albion), Hartson (Celtic).Reuse content