Fernandes, who teed up Marcus Rashford's opener at the King Power Stadium on Boxing Day, thought he had secured the points for United when he struck home after latching onto Edinson Cavani's pass with 11 minutes remaining.
It took Fernandes onto double figures in league goals for the season.
That made him the first player from Portugal to score 10 or more in a single campaign in England's top-flight since former United star Ronaldo did so in 2008-09, when the winger netted 18 times.
Fernandes has had a direct hand in over half of United's Premier League goals since his debut (31/60), scoring 18 and assisting a further 13.
However, United, who were looking to match Chelsea and Manchester City's record of 11 consecutive away Premier League victories, were pegged back for a second time in the 85th minute – Jamie Vardy sweeping in via a deflection from Ayoze Perez's cross.