The Qatari outfit, who reached the quarter-finals of last season's competition, took the lead thanks to a 35th-minute strike from midfielder Nam Tae-Hee.
Lekhwiya's lead was doubled through an own goal from Habieb Mehdi Nasief shortly after the interval, and the defender then scored what proved to be little more than a consolation for the Bahraini club on the hour mark.
Muang Thong United are also through to the next stage following a 2-0 victory against Ha Noi T&T in an ill-tempered affair.
Macedonian midfielder Mario Durovski opened the scoring for the Thai outfit after 35 minutes before Sam Gallagher was sent off for Ha Noi 11 minutes into the second half.
Former Cardiff City and QPR striker Jay Bothroyd doubled Muang Thong's advantage shortly after as the hosts all but ensured progress.
Substitute Artit Daosawang saw red as Muang Thong were reduced to 10 men four minutes into injury time, with Hoang Vu Samson then becoming the second Ha Noi player to be dismissed a minute later for a second bookable offence.
South Korean midfielder Go Seul-Ki scored a hat-trick to inspire El Jaish to an easy 5-1 success against Nasaf of Uzbekistan.
Brazilian striker Nilmar and defender Abdulrahman Issa also found the net for the hosts, while Farrux Sayfiyev scored a consolation for Nasaf.
Elsewhere, Kuwaiti side Al Qadsia cruised into the next round with a comprehensive 4-0 triumph against Bani Yas of the United Arab Emirates.
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