The bird became lodged in the front of Lorenzo’s Yamaha, forcing him into the pits during Saturday’s final qualifying session. He returned to clock the fastest qualifying lap of 1 minute, 27.899 seconds, beating the Phillip Island lap record by 0.766 seconds.
It was the 26th pole of his career and his third this season.
Marquez holds a 43 point lead over Lorenzo and needs to finish eighth or better to clinch the championship on Sunday.
Valentino Rossi will share the front row after qualifying in third place ahead of Alvaro Bautista, Dani Pedrosa and Cal Crutchlow on the second row.