Marcos Rojo partnered Chris Smalling at the heart of United's defence as Jose Mourinho's men won 2-0 to remain in 2nd place in the league table.
There were some suggestions that Mourinho may have dropped Jones after his comical midweek own goal against Tottenham, when he side-footed in from Kieran Trippier's cross to condemn United to a 2-0 defeat at Wembley.
However, it would seem harsh to drop Jones from the squad entirely for what was merely an unfortunate accident, and sure enough the defender's sister confirmed that he had been missing due to sickness.
"Hope everyone feels better soon; including Phil Jones. There are a lot of bugs going around lately!" she wrote.
Until Saturday, Jones had played every game for United since missing their 2-1 home defeat to league leaders Manchester City in December. The loss to Tottenham on Wednesday was United's first league defeat since then.
Saturday's match was an ideal one for Jones to miss, as Huddersfield posed little threat to the Manchester United defence. They held out resolutely until after half-time before Romelu Lukaku opened the scoring, and then Alexis Sanchez got his first for the club with a penalty rebound.
Jones will be expected to return for United next week when they travel to St James' Park to take on Newcastle.