The Clarets had kept the away side's dangermen at bay for the majority, but left the South Korean international completely unmarked from Erik Lamela's corner in the 75th minute.
Harry Kane, who flicked on the set-piece to claim another assist, had cleared James Tarkowski's header off the line at the other end moments earlier.
Jose Mourinho's side climbed up to fifth as a result while the Clarets, with a solitary point from five games, remain in the bottom three.
1. Nick Pope 6
Had been a mere bystander for the most part, until Son opened the scoring. In constant communication with his defence and gathered everything that came his way with authority.
2. Matt Lowton 7
Wasn't given the easiest of tasks on his re-introduction to the side, but stood up to the threat of Ndombele and Son exceptionally well. Rarely put a foot wrong in an assured defensive display and got forward well.
3. Charlie Taylor 7
Stretched by Moura when the Brazilian was left one-on-one, but tracked the forward well and restricted his opportunities to cross the ball or play infield. Reduced the threat down his side of the pitch and combined well with McNeil.
4. Kevin Long 7
Another bright display from the Republic of Ireland international. Mopped up spillages in and around the penalty area, strong in the air and made a superb block to deny Son as he'd just pulled the trigger in the second half.