Leif Davis put the Tractor Boys into the lead after 29 minutes with a fine, first-time finish.
Fernandes restored parity with his first goal five minutes before the break, before a Jacob Greaves own-goal handed the home side the lead after 56 minutes.
From then on in it was all United as Fernandes scored from the penalty spot on 61 minutes before completing his hat-trick with a composed close-range goal.
Bryan Mbeumo put the result beyond doubt with his chip over a beleaguered Kjell Scherpen in the Ipswich goal, with eight minutes of the match remaining, although the last goal arrived in injury time as substitute Chuba Akpom slotted home from close range.
United fans would have been worried to see their side concede the opening goal after starting their season with a shock 2-0 reverse to fellow promoted side Hull City at the MKM Stadium last weekend.
But after a strong first half from Gary O'Neil's charges, it was the home team who ran out deserved winners after a dominant display.
The result saw Man Utd end the evening in 10th place on the league standings with three points, and left Ipswich in 12th, also with three points following an opening day 2-1 win over Sunderland.
The first shot of the game was hit by Marcus Rashford from distance but his effort hit a foot and looped up kindly for Kjell Scherpen in the Ipswich goal.
A neat-one two with Matheus Cunha and Rashford set the former up for a shot that was always rising over the target.
Daizen Maeda produced a run of his own and hit Ipswich's first effort of the game, but without enough power to trouble United goalkeeper Senne Lammens.
Diogo Dalot curled a left-footed shot towards the top corner after a flowing move from United involving both wingers, but Scherpen made a super save.
Lammens then needed to be alert to deny Enciso after a quick break forward, while Rashford was inches away from sliding in to meet Cunha’s low cross as the Red Devils raced up the other end of the field.
A 20th minute Rashford free-kick wasn't too far from sneaking in the goal, while Fernandes hit the defensive wall with his set-piece moments later.
But it was Ipswich to take the lead in this end-to-end encounter with Davis slamming the ball into the roof of the net after a strong run and cut back from Abdul Fatawu.
United though were soon back in the game after a slip on the ball in midfield from Marcelino Nunez allowed Matheus Cunha to pick up the ball and play in Fernandes, who fired in past Scherpen with a fine left-foot finish.
There were calls for a penalty as Youri Tielemans went down in the box under a challenge from Dara O'Shea but the referee waved play-on.
Lisandro Martínez then fired just over the target from range as he looked to fire the home side into the lead ahead of the half-time break.
There was only one change at half-time as Akpom came on for Emersonn for Ipswich.
Enciso's effort just after the break was high as he drove forward with purpose, while Mbuemo thought he had scored on 53 minutes when he connected to a volleyed Rashford cross from the left, but the ball hit the knee of the striker before slamming off the face of the crossbar and was ultimately bundled out of play.
The move ultimately ended with Tielemans firing tamely at Scherpen after a corner.
But United were soon in the lead, for the first time in this game, with 56 minutes played as Harry Maguire fired in from just inside the 18-yard area, although the shot took a massive deflection of O'Shea and was counted as an own-goal. There were calls for handball, but after a brief VAR check, the goal was given.
The drama continued after the restart as Cunha was brought down in the box by Jacob Greaves, after a superb through ball from Kobbie Mainoo, and Fernandes made no mistake from the penalty spot with an expertly dispatched spot kick.
Exequiel Palacios was introduced for Nunez after the goal for his Premier League debut.
Scherpen made an important save just past the hour mark to keep out a powerful Rashford volley at his near post, but there was seemingly no stopping a rampant Man Utd side as Fernandes completed his hat-trick with a tap-in in the 68th minute. Mainoo and Mbeuma both had shots blocked inside the area but Fernandes made no mistake when the ball fell kindly on his right boot.
Fernandes nearly scored a fourth from the centre circle but his swerving lob landed on the roof of the net.
Ipswich looked to get back in the game with the introduction of Daniel Furlong and Abdoul Ouattara for Maeda and Sasa Lukic, while with the match potentially already in the bag, Michael Carrick brought on Noussair Mazraoui and Leny Yoro for Shaw and Dalot.
Scherpen used his body to deny Cunha as United pressed for another goal following some more good approach play by Rashford. The United winger was given a roar of approval from the home fans after tracking back into his box to make a strong tackle - but it proved to be his last touch of the ball as he made way for Patrick Dorgu, as Benjamin Sesko replaced Cunha and Andrew Santos took the field instead of Mainoo.
But Carrick's team were not done as Mbuemo lobbed an advancing Scherpen, with his ball bouncing into the net after hitting the crossbar, but it was the quality of Fernandes' looped pass that allowed the Cameroon frontman to pick his spot.
There was still time for one more goal though as some sloppy defending from Martínez allowed Enciso to steal the ball and fire in a low cross that was turned in by Akpom.
Ipswich had been excellent for as long as an hour but ultimately had no response from a dominate United display, that will give them plenty of confidence heading into next week's trip to Everton, as Ipswich next take on Liverpool.
