The AFC Player of the Year has not featured in the Champions League since being banned for eight matches for headbutting and spitting at Western Sydney Wanderers defender Matthew Spiranovic in the final last November.
Al-Shamrani made up for lost time on Wednesday, though, opening the scoring in the first minute of the second half to take his tally in the competition to 26 - having previously been level with Dong-Gook Lee.
Yasir Al Shahrani added a second goal for the Saudi Premier League outfit as last year's runners-up leapfrogged Al Sadd on goal difference with two group games remaining.
Lokomotiv made amends for their thrashing at Al Sadd last month by dishing out a 5-0 hammering to the Qatari outfit to enhance their chances of qualifying for the last 16.
The Uzbekistan side lost 6-2 in Doha last month, but gained revenge on Wednesday as Al Sadd lost for the first time in Group C. They are now just three points ahead of Lokomotiv.
Marat Bikmaev's double put Vadim Abramov's men in control at the break, and further goals from Sanjar Shaakhmedov, Damir Kojasevic and Ruslan Koryan rubbed salt into the 2011 champions' wounds.
There was a goal-fest in the Group E encounter at Jinan Olympic Sports Centre, where China's Shandong Luneng and Japanese outfit Kashiwa Reysol drew 4-4.
Reysol led 3-1 just after the half-hour mark after Wang Yongpo had given the home side an early lead, but Junior Urso and Walter Montillo struck to make it 3-3 at the break.
Yang Xu's penalty put Cuca's side in front for the second time, but a howler from goalkeeper Wang Daleien enabled Cristiano to salvage a point with his second goal of the game to ensure Kashiwa sit second - still four points better off than their opponents.
Jeonbuk Motors remain top of the group on goal difference, but Abass Cheikh Dieng's stoppage-time strike salvaged a 1-1 draw for Binh Duong.
Group G leaders Beijing Guoan missed the chance to secure their passage into the last 16 when they were held to a 1-1 draw at Urawa Reds, while second-placed Suwon Bluewings moved three points clear of Brisbane Roar after toppling the A-League side 3-1.
Persepolis hold a two-point lead at the top of Group A after beating Al Nassr 1-0, with Lekhwiya up to second following their victory over Bunyodkor by the same scoreline.
