The Portuguese star scored twice in the Red Devils 4-1 rout of Istanbul Basaksehir at Old Trafford on Tuesday evening - with Rashford's spot kick and Daniel James' late strike putting the finishing touches on a solid performance.
Fernandes' two goals came in the opening 20 minutes as Ole Gunnar Solskjaer's side got off to a flying start, but when Rashford was felled in the penalty area, the ex-Sporting attacker handed the ball to his team-mate to get on the scoresheet instead of going for the hat-trick himself.
With Fernandes scoring from the spot in United's last match against West Brom, the playmaker revealed he had agreed to give Rashford the next penalty and said it was important the England international maintained his confidence.
"Of course every player wants a hat-trick," Fernandes told BT Sport post-match.
"But after the game in the Premier League I told Rashford that he could take the next one so I remembered that and also he's one of the top scorers in the Champions League so it's important for him to get the confidence.
"It doesn't matter who takes the penalty as long as the team scores."
It took United just seven minutes to begin the scoring, and they did so in style, Fernandes lashing a ferocious half-volley in off the crossbar from just outside the box after Basaksehir partially cleared a corner
The Portugal international was in the right place at the right time 12 minutes later, on hand to tap in from close range when Basaksehir goalkeeper Fehmi Mert Gunok inexplicably spilled a routine cross.
It seemed like Fernandes would step up to the spot to score this hat-trick on 35 minutes after Rashford was fouled by Boli Bolingoli, but instead he gave the ball to the latter, who slotted the penalty into the bottom right corner.
Despite Deniz Turuc pulling a goal back with a brilliant free kick on 75 minutes, James finished the match in stoppage time - finishing off a sweeping counter-attack move by side-footing Mason Greenwood's cross into the back of the net.
"I think we played really well," Fernandes said about performance.
"We started the game with the right mentality - strong, intense. First half was important to get three points today.
"We're in a good position but can't relax - we have to think of the Premier League now and win the next game on Sunday and after that we don't have much time but we have some time to think of the next Champions League game.