Probierz makes the decision in the wake of removing the captaincy from Lewandowski and handing it to Inter Milan midfielder Piotr Zielinski.
The move saw Barcelona striker Lewandowski announce he was quitting the Poland team until Probierz left his job.
A poor 2-1 World Cup qualifying defeat to Finland on Tuesday increased the pressure on Probierz, who announced his resignation this morning.
Greatest honour of my life
"I have come to the conclusion that in the current situation the best decision for the good of the national team will be my resignation from the position of coach," Probierz said in a statement.
"Performing this function was the fulfilment of my professional dreams and the greatest honour in my life."
He added: "Thank you, of course, to all the footballers I have had the pleasure of meeting along the way.
"I will keep my fingers crossed for all of you, because the national team is our common national asset."