It is the second time in 19 months that crowd issues have arisen during this fixture in South Yorkshire, with the Reds 3-2 victory over United in January 2017 also featuring ugly scenes off the pitch.
Today, Eddie Nketiah stepped off the bench to score late on for Marcelo Bielsa's side before a Mateusz Klich penalty secured all three points for the visitors in a 2-0 victory which sent Leeds back to the top of the Championship.
The Arsenal loanee bagged six minutes from time which sparked wild celebrations in the away end behind the goal, where 4,400 Whites supporters were housed.
Minutes later United fans could be seen clashing with stewards, one of whom was escorted away having becoming embroiled in the trouble.
A separate incident then occurred; a number of away fans clashing with home supporters in the East Stand.
United head coach Bielsa called the crowd trouble "a pity" during his post-match media duties and the club are yet to make any official comment.
Barnsley FC have said they are looking into the incidents.