First half strikes from Bojan and Marko Arnautovic sunk United and gave Mark Hughes' Stoke some Boxing Day cheer at the Britannia.
It was a seventh game without a win for Louis van Gaal's side and- despite an improved second half showing- the Reds were unable to find a fightback and crashed to a fourth successive loss.
The Reds left captain Wayne Rooney on the bench (bringing him on at half time), and the 30 year old's introduction did at least have an impact as the visitors played with better urgency at a greater tempo after the break.
Despite that, Van Gaal is now a man under serious pressure and Stoke took full advantage as they started well and went ahead in the 19th minute.
Glen Johnson was gifted a late Christmas present when Memphis Depay attempted to head back to David de Gea but failed to muster enough power allowing the Stoke man to intercept and set up Bojan for a simple finish.
Seven minutes later, it was 2-0 when Marko Arnautovic blasted home a 25-yarder after Bojan's free-kick had come back off the United wall.
The Austrian, whom gave Ashley Young a torrid time, then should have made it 3-0 when clean through before the hosts keeper Jack Butland saved well from Juan Mata.
Marouane Fellaini should have done better with a header and Anthony Martial was denied by another good save from Butland- during an improved second half for the visitors.
Stoke remained a threat themselves though and almost rubber-stamped the result through the impressive Bojan, whom forced a smart save from De Gea.
Substitute Charlie Adam went close with a free-kick and former United man Mame Diouf headed over, but despite a late rally the Reds were unable to find a way back.
A fourth consecutive loss for the Reds then - our worst run of form for nearly 40 years - ahead of United's final match of 2015 at home to the champions Chelsea on Monday.
Overall team performance: 2/10
United Faithful Man of the Match: United's travelling fans who again did the club proud singing until the end