The Red Devils were hoping to build on their mid-week win in the Europa League having lost last weekend in the local derby.
However, it was the Toffees who opened the scoring as early as five minutes into the game as Super Eagles star Alex Iwobi scored via a superb finish from outside the box to give Everton an early 1-0 lead in the game.
But Ten Hag's men would find a response later after a brilliant finish from Antony in the 15th minute to level matters at Goodison.
United then grew into the game and continued to dominate with the better chances coming their way.
However, Erik ten Hag had to make a tactical change in the 29th minute with Anthony Martial who assisted Antony's for the equalizer making way for Cristiano Ronaldo.
The substitute will then go on to complete the comeback in the first half after being played through by Casemiro in the 44th minute to give the Red devils a 2-1 lead.
Ronaldo's strike in the first half now meant that he has taken his goals in European club football career to an incredible 700.
The Portuguese striker's goal would prove the final action in the first period as United went into the break with a slender but deserved advantage.
The second half resumed and United continued to dominate proceedings as they pushed for a third.
However, after a series of opportunities, the Red devils thought they had finally put the game to bed in the 80th minute after a brilliant effort from Marcus Rashford.
But the 24-year-old's effort was ruled out by VAR after a handball in the build-up.
At the end, Erik Ten Hag's men held on for a deserved 2-1 win at Goodison Park as Frank Lampard's men fell short against the Red devils on Sunday night.
Social Media Reactions
Following the win for Manchester United, fans have taken to social media to congratulate Portuguese superstar Cristiano Ronaldo on his incredible achievement.
Ronaldo became the first player in history to score and incredible 700 career club goals with his effort against Everton.
Here's how fans have reacted below: