Sebastian Soria put the home side ahead only for Al Wakra to turn it around with goals from Moaz Yousif Adam and Younis Mahmood.
Lekhwiya earned a share of the spoils, though, when Ali Afif netted midway through the second half.
The draw meant Al Wakra moved clear of Al Rayyan at the summit although they have played a game more.
Qatar CC earned their first win of the season at the fourth attempt with a 2-0 victory at Al Arabi courtesy of a Seyed Hadi Aghily Anwar penalty and a Bakary Kone strike.
Al Khrityat and Umm Salal drew 1-1.
Yahia Kebe put Al Khrityat in front early on but Mamadou Traore levelled after 28 minutes.