The two players were criticised for their rendezvous with the president of Turkey in London, which the German Football Federation put down to an "election campaign stunt".
Gundogan was subsequently subjected to jeers from German supporters during both of their recent World Cup warm-up matches against Austria and Saudi Arabia.
Effenberg, who was sent home from the 1994 World Cup after the group stage for directing an obscene gesture in the direction of his own supporters, believes that the duo have benefited from the DFB's inconsistency.
"If you bet on certain values, as the DFB repeatedly conveys, then the decision can only be made by throwing the two players out," Effenberg is quoted by the Manchester Evening News as saying.
"Ozil and Gundogan have now been lucky that the DFB acted in this case in an inconsistent way, and not quickly.
"[Booing] is the worst thing that can happen to you. Because you're asking yourself a lot of questions, like the value of wearing this jersey."
Germany face Mexico in their World Cup Group F opener on Sunday.