United cruised to a 4-0 win over Everton without the Frenchman, but Mkhitaryan believes they are finding it “hard to play” without him.
The playmaker stated that his side will find it “very difficult” to maintain their early season form whilst Pogba remains on the sidelines.
Meanwhile, Jose Mourinho has branded a report that his £89million singing could be out for up to 12 weeks as “completely nonsense information”.
"It's hard, because he's a top player for us." Mkhitaryan told SFR Sport.
"It's going to be very difficult, but the coach knows how to make up for that and we're going to help him come back stronger."
Daley Blind is sad that Paul Pogba is injured
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Mourinho doesn't know how long he'll be without Pogba
The Armenian scored his side's second goal as they rallied late-on to secure a convincing 4-0 victory over Ronald Koeman's Tofees at Old Trafford on Sunday.
The match also saw the highly anticipated Old Trafford return of Mkhitaryan's former teammate Wayne Rooney, and the ex-Borussia Dortmund player was happy with the respectful reception the club's record goal-scorer received.
"Rooney is a legend. He's an exceptional player. It's a shame that he's at Everton now," he added.
Pogba will undergo further scans this week to determine the full extent of his hamstring injury.
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Mkhitaryan is concerned for United's fortunes in Pogba's absence
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But Mourinho reiterated there was not yet a definitive timeline on the midfielder's recovery, with United still to learn how long they will be without him.
"I don't know if it's 12 weeks or 12 days, honestly," he said.
"The player was diagnosed initially after the match and, because of the conditions of the muscle and bleeding, the decision was one more week to wait and see clearly in the scans.
"Nobody in this club spoke about 12 days or 12 weeks. It's a muscular injury in the hamstring, but we have a normal procedure and wait a few more days.”
