Sesko is yet to start in Carrick's six matches in charge, but has come off the bench to net in three of his last four appearances with vital goals.
The 22-year-old also scored a late winner against Fulham and rescued a point against West Ham deep into stoppage time in United's previous outing.
Sesko started the move that led to the winning goal as all of United's £200 million trio of attacking signings last summer combined to great effect.
Matheus Cunha picked out the run of Bryan Mbeumo, who squared for Sesko to slot home his sixth goal in seven appearances since Ruben Amorim was sacked in January.
Victory lifted United into the Premier League's top four, three points clear of Liverpool and Chelsea in the battle for a place in next season's Champions League.
"It was a ruthless finish, I like the way he put it away with real confidence," said Carrick, who has five wins and one draw since taking charge at Old Trafford.
"Great play from Matheus and Bryan to set it up. Delighted for Ben again, coming on and making the difference."
United did not hit the height of sparkling performances to beat title challengers Arsenal and Manchester City in Carrick's first two matches in charge during an uninspired clash at the Hill Dickinson Stadium.
But the former Middlesbrough boss was delighted with a third clean sheet in six games.
United had held opponents goalless just twice in 29 matches this season before Carrick's arrival.
"We had to do a lot of work. Credit to Everton they made it difficult, made us defend our box a lot. The spirit with which we defended the box was top class," added Carrick.
Goalkeeper Senne Lammens made a couple of vital saves to continue an impressive debut season at United for the 23-year-old Belgian.
"Senne was outstanding tonight," said Carrick. "You couldn't hope for much more from a goalkeeper. It was an exemplary performance, so delighted for him.
"You want (a goalkeeper) to take the chaos away and Senne is that. That calmness and composure helps those in front of him."