The 24-year-old was inked on Monday but his arm suffered an infection, ruling him out of next Saturday's German Cup final meeting with Borussia Dortmund.
Frankfurt had been looking to extend Varela's season-long loan deal by another year, but they have now taken the decision to cut it short and instead send him back to Old Trafford early.
"The club cannot tolerate that a player would defy instructions," said sporting director Fredi Bobic. "We'd been thinking about a loan extension. But that won't happen. He'll be suspended with immediate effect."
Varela made 10 competitive appearances for Frankfurt upon joining last summer, appearing in each of the last five league and cup games.