The Socceroos meet Paraguay at the Sydney Football Stadium on Saturday but will be without Neill, who injured himself whilst playing for Turkish club Galataaray on Friday.
Thwaite, who is in his first national team squad in three years, says having a central defender out of the team provides a great chance for players like himself to prove themselves at international level.
"It's the coach's decision but I would be honoured to take on the role at centre back, especially in place of Lucas,'' Thwaite said on Tuesday.
"Lucas hasn't missed too many games so these opportunities don't come around often and we need to take full advantage of it.''
And Thwaite said it was great that new Socceroos coach Holger Osieck was putting more emphasis on using A-League players in his squad than previous boss Pim Verbeek.
"It's a breath of fresh air,'' he added.
"He has put in a new initiative to go to all the A-League clubs and meet all the players personally.
"Every second coach has a different opinion.
"For the future of Australia in general I think the A-League needs have to become bigger.
"The more representatives we have in the national team the better the A-League will become.''