When security did not immediately intervene, at least three other pitch invaders joined in and play did not restart before referee Neil Doyle blew for full-time.
The match, the first game of association soccer at the home of the Gaelic Athletic Association since 2009, was played in front of a sell-out crowd of more than 80,000.
It ended 1-1 at the end of 90 minutes after Joshua Zirkzee gave United a 16th-minute lead before Leeds equalised just before the half-hour mark, with Brenden Aaronson scoring after good work from former United winger Daniel James.
Noussair Mazraoui scored the decisive spot-kick as Manchester United won 5-4 in a penalty shoot-out.
"First half we were really dangerous and could've had a number of goals," United manager Michael Carrick told ITV. "We played some really good football.
"They came back into the game, and in the second half there were a few changes and it was important to get some minutes in some of our lads.
"The young lads did well, it was everything we expected of them. Winning the game is always nice."
Fernandes missed from the spot before it went to sudden death, but after James Justin's effort struck the crossbar, Mazraoui saw United to victory.
Lisandro Martinez, Kobbie Mainoo and Marcus Rashford were among those watching on, not involved after only joining the training camp at the start of the week following the World Cup.
Before the match, Carrick said he was holding the trio "in reserve" for Saturday's friendly against former boss Ruben Amorim and AC Milan in Wroclaw, Poland - potentially Rashford's first appearance in a United shirt since December 2024.
"He's our player," said former United and England midfielder Carrick of Rashford, now back at Old Trafford after a loan spell at Barcelona.
"He's come back great, like any other player. I've known him a long time, he gives us something a bit different.
"He's been in great spirits since he's come back."
After several half-time changes, including a debut for United's new 18-year-old winger Tynan Thompson, Leeds should have gone ahead six minutes in when Joe Rodon's low cross found Harry Wilson, but the summer signing shot straight at Senne Lammens.
Fernandes was among six United players to come onto the field on the hour and, having seen one effort ruled out for offside, he hit the crossbar with a curling shot five minutes from time.
Get ready for the new Premier League season
The Premier League returns on Friday, August 21st as defending champions Arsenal host new boys Coventry in the 2026/27 curtain-raiser.
Get ready for kick-off ahead of the new season:
- Transfer Tracker: All the latest done deals and rumours
- Premier League fixture list revealed for 2026/27
- All Premier League and top European club kits for the 2026/27 season
