The 2013 quarter-finalists scored three second-half goals on their way to a comfortable 4-1 victory over Al Kuwait.
Sebastian Soria opened the scoring shortly prior to the half-hour mark, before Javad Nekounam levelled from the spot five minutes later.
Youssef Msakni found himself in plenty of space to slot the ball into the bottom right-hand corner midway through the second half to re-establish Lekhwiya's lead, before Karim Boudiaf and Luiz Junior put the game beyond doubt - Msakni providing the assist for both.
Three goals in 18 first-half minutes left Chonburi reeling, and Shao Jiayi completed the job with an 89th-minute strike, before Thiago Cunha was given his marching orders at the end.
The remaining Champions League berth went to Australia's Melbourne Victory, who edged a tight encounter against Muangthong United 2-1.
The Thai side broke the deadlock via a close-range header from Macedonian Mario Durovski in the 22nd minute, before Melbourne's Mark Milligan saw a penalty kick saved.
