Shojaei and his Iran team mate Ehsan Hajsafi played for Greek side Panionios against Israel's Maccabi Tel Aviv in a Europa League qualifier earlier this month, prompting Iran's deputy sports minister to declare the pair were banned from the national side.
Iran does not recognise the state of Israel and bars its athletes from competing against participants from the country.
Hajsafi, however, was included in the squad to play South Korea in Seoul on Aug. 31 and Syria at home on Sept. 5.
Top of Group A in Asia, Iran have already qualified for next year's finals in Russia.
A member of Iran's squads at the 2006 and 2014 World Cups, Shojaei captained the team in their last qualifier, a 2-0 win over Uzbekistan in June which secured their ticket to Russia.
Queiroz said he had included younger players in his squad but 33-year-old Shojaei and other excluded veterans remained part of his plans in the leadup to next year's finals.
"We have a 37 Elite Player Group that is our preparation basis for the World Cup and this call-up list, bringing some younger players, reflects our strategy of working on all this Elite Group," Queiroz wrote on his Facebook page.
"This doesn't mean we are in condition to (leave) behind experienced players that we are used to have with us, like Pejman (Montazeri), Masoud (Shojaei), (Andranik) Teymourian or (Khosro) Heydary, who continue in this 37 Elite Player Group as important options for Team Melli."
Queiroz said on his Facebook page on Saturday that his team was facing "dangerous winds of havoc" and complained that Irani authorities had failed to provide adequate financial support for their World Cup campaign.
"Team Melli spirit and mentality has always been, no matter what, 'under promise and over delivery'," he wrote.
"However, it is not understandable and acceptable that Team Melli (still) get rewarded, as usual, with nothing but 'over promises and under deliveries'."
Alireza Haghighi, Alireza Beiranvand, Hamed Lak, Seyed Jalal Hosseini, Morteza Pouraliganji, Ramin Rezaeian, Vouria Ghafoori, Milad Mohammadi, Mohammad Ansari, Saeid Aghaei, Roozbeh Cheshmi, Ehsan Hajsafi, Ashkan Dejagah, Alireza Jahanbaksh, Vahid Amiri, Saeid Ezatolahi, Mehdi Torabi, Ali Karimi (Unattached), Saman Ghoddos, Karim Ansarifard, Reza Ghoochannejad, Sardar Azmoun, Mehdi Taremi
(Writing by Michael Church; Editing by Ian Ransom)