Players from both teams wore black armbands and stood around the centre circle.
With many of the 71 victims members of Brazilian top-flight team Chapecoense, the tragedy brought back memories of the 1958 Munich air disaster, in which eight United players died.
Players from both teams wore black armbands and stood around the centre circle with their arms around each other during a silence that was impeccably observed.
"The thoughts of everyone at Manchester United are with @ChapecoenseReal and all those affected by the tragedy in Colombia," United wrote on Twitter after the accident.
United's line-up featured Spanish goalkeeper David de Gea, who played alongside Cleber Santana, one of the victims of Tuesday's crash, at Atletico Madrid.
"Deeply affected by Medellin's plane crash. I shared (a) locker with Cleber Santana and it's difficult to reveal how I feel," De Gea wrote on Twitter. "Rest in peace amigo."
The Munich crash tore the heart from a youthful United team dubbed the 'Busby Babes' in honour of manager Matt Busby.
Their plane crashed on a slush-covered runway in Munich after refuelling on its way back to England after a victorious European Cup quarter-final against Red Star Belgrade.
The dead included United midfielder Duncan Edwards, seen as a future England great, as well as three members of club staff and eight journalists.
Busby survived the accident and rebuilt the team around fellow survivor Bobby Charlton, eventually leading United to European Cup glory against Benfica in 1968.