The centre-back bundled Eden Hazard over in the penalty area, picking up a yellow card in the process, with the Belgian brushing himself off before slotting the spot-kick past David de Gea.
Jones was chosen in the starting XI ahead of Eric Bailly by United boss Jose Mourinho, leaving some fans wondering why the error-prone defender was selected in such an important game.
Former England captain Alan Shearer admits he would have enjoyed the opportunity to come up against Jones during his own playing career.
"If I was a centre-forward playing against Phil Jones going into a game for 90 minutes, I would feel confident he would make at least one mistake in the game that I could pounce on,” the ex-Blackburn and Newcastle striker told the BBC.
"It's a last-ditch tackle, it's his mistake in the first place for letting [Hazard] get in there. But it is a genuine attempt."
England supporters were also concerned by Jones' poor tackle following his inclusion in the Three Lions' squad for the World Cup, where Gareth Southgate's men take on Belgium and Hazard in the group stage.
Red Devils and England fans took to Twitter to express their disappointment in Jones, urging Southgate to look elsewhere for defensive cover in Russia.
I’ve been saying this for ages but a blind horse would be an improvement on Phil Jones. — Elko Born (@Elko_B) May 19, 2018
My manager leaves Eric Bailly, our best CB, on the bench, whilst still playing Chris Smalling and Phil Jones. I give up. — Ryan. 🔴 (@Vintage_Utd) May 19, 2018
Phil Jones giving us a preview of things to come in the World Cup — Footy Humour (@FootyHumour) May 19, 2018
Phil Jones, what a donkey that lad is! — LFC Stanley House 🇺🇦 (@LFCStanleyHouse) May 19, 2018
Phil Jones may have a few good games every now and again but at the end of the day, he'll always be Phil Jones. — JoshGI 🇾🇪 (@JoshGI97) May 19, 2018
Gareth, if you’re watching mate, let’s not start Phil Jones at the World Cup please. Especially not against Belgium 🇧🇪 — The Football Ramble (@FootballRamble) May 19, 2018
Phil Jones has gifted Chelsea the FA Cup.— 👑 DaddyMo PhD CEng 👑 (@officialdaddymo) May 19, 2018
Phil Jones is going to the World Cup.... — ManUnitedZone (@ManUnitedZone_) May 19, 2018
Jones almost made amends for his mistake just before half-time, but could only head wide following an excellent cross from Ashley Young.