The Chilean had only just returned from a hamstring issue, and it appears to be a recurrence of the same problem, with the former Arsenal man pointing to the back of his leg as he pulled up on 64 minutes before being replaced by Marcus Rashford.
Speaking after the match, interim boss Ole Gunnar Solskjaer expressed his hope that the injury wouldn't be a serious problem, with Sanchez making what was his first start for the club since November 7.
"I think [Alexis] will be OK," the Norwegian told BT Sport, "but he was tired and hopefully it is not a bad reaction, so we will see once we get closer to next week.
"We are going to have some days to recover and then train hard because we know that if that performance is repeated at Wembley against Spurs, we are not going to come back with a clean sheet and any points."
Sanchez - who was making his first start under Solskjaer - made his way towards the bench and not down the tunnel after he was withdrawn, before accidentally taking his new manager's seat.
United's No.7 provided the assist for his side's second goal, sliding the ball through for Romelu Lukaku - also starting for the first time under the new boss - who rounded Anssi Jaakkola and slotted home from an acute angle.
Just two minutes before Sanchez's injury, Juan Mata - scorer of United's first goal from a penalty awarded by VAR once Fred's strike was disallowed - made way for 19-year-old Tahith Chong to make his competitive debut for the club.
Despite Reading dominating the ball with 60% possession, the Red Devils would ease to a 2-0 win to make it five wins in five under Solskjaer.
United have also scored 16 goals during Solskjaer's time in charge although will expect a tougher test at Wembley as they face Tottenham in the Premier League in their next fixture.
Reading, meanwhile, will look to bounce back from their FA Cup elimination as they host play-off chasing Nottingham Forest in the Championship.
United will find out who they will face in the fourth round on Monday night, when the draw takes place.