Despite the loss the group is the tightest in Asia, with the Mariners in fourth place, just two points below the group leading Beijing.
Beijing were the dominant force at the Workers’ Stadium, getting started just six minutes in as Peter Utaka forced two pieces of defensive work, first a good save, low, from Liam Reddy before Eddy Bosnar managed a last ditch tackle.
The Mariners best chance came in the 30th minute as Bernie Ibini got a half-chance from a volley that he sent high and wide.
Outside of that chance it was all Beijing and they should have hit the lead as Yu Yang was left wide open and found by a cross which he headed in to the ground and over the bar.
Shao Jiayi could well have given Beijing a lead in stoppage time as he was set up by a superb Zhang Chengdong pass but his effort was much too tame.
It mattered little as Shao made ammends just one minute later, as he ran in on goal and launched a powerful strike that snuck in between Reddy and the near post, giving the hosts a 1-0 lead at the break.
At half time Beijing made an important change, introducing Dae-Sung Ha to help control midfield alongside Darko Matic.
Eddie Bosnar looked to pull off more free-kick magic in the early stages of the second half but his effort was dealt with by the Chinese side.
The Mariners were severely punished for that miss as Beijing doubled their lead with Shao sending a ball through for Utaka, who rounded Reddy and slid the ball in to the back of the net.
The Mariners went for the match in the closing stages, and in the 84th minute got a lifeline as Isaka Cernak was brought down in the box, allowing Nick Fitzgerald to step up and slot the penalty.
That made for a tight finish, but Beijing were never really troubled as they held on for the 2-1 win that moved them to the top of the group.