The 28-year-old has endured a tough season and made the last of eight appearances in January's FA Cup fourth-round win at Tranmere.
Jones has been absent since football resumed after the coronavirus suspension through injury but was named in United's 30-man squad for the Europa League final eight tournament in Germany.
However, the defender will not feature in the quarter-final against FC Copenhagen or beyond due to a knee issue that has seen him remain in Manchester.
"Phil has been following an individualised training programme during the post-lockdown period to optimise recovery from a knee problem," United boss Solskjaer told the club website.
"It was a good opportunity as we had sufficient cover in defensive positions for the remaining Premier League games and he will continue to work with a fitness coach at the Aon Training Complex, while the squad are in Germany."