It was the home side who started brightly and they could have found themselves two goals up after the first few minutes but Hernandez and Danny Welbeck allowed chances to go begging.
Reading managed to settle into the game but United always looked the more dangerous of the two teams in the first-half and almost took the lead before the break, when substitute Nani struck a fine effort but it hit the outside of the post with Adam Federici beaten.
The second-half started much like the first with United on top but they had to wait till after the hour mark before they broke the deadlock.
Nani, who looked dangerous after coming on for Phil Jones in the first-half, got a shot away on the 69th minute and having taken a deflection it got the better of Federici.
It was only three minutes until United doubled their lead when goalscorer Nani turned provide by producing a fine cross for Hernandez, who headed to ball into the back of the net.
Just as the home side thought they were home and dry the Royals got themselves back into the game when Jobi McAnuff took advantage of some poor United defending to score with a simple finish on the 81st minute.
Reading striker Adam Le Fondre had an opportunity in injury-time to get the visitors level but his header was deflected wide by Chris Smalling, as United held on and booked themselves a place in the next round of the FA Cup.
A goal apiece from James Tomkins and Luka Milivojevic handed Crystal Palace a crucial 2-0 win over Huddersfield at the John Smith's Stadium on Saturday evening.
Manchester United bounced back from their Champions League exit as they beat Brighton 2-0 at Old Trafford on Saturday night to reach the FA Cup semi-finals.
Tottenham reached the FA Cup semi-finals after they cruised to a 3-0 victory over Swansea in their quarter-final clash at the Liberty Stadium on Saturday.
Premier League basement club West Brom squandered the lead as they suffered a 2-1 defeat to Bournemouth at the Vitality Stadium on Saturday.
Chesterfield boss Jack Lester felt his side were unlucky not to claim all three points after their 1-1 draw at Cheltenham.
New Swindon manager Phil Brown revelled in his side's victory at Cambridge in his first game in charge.