The mercurial Portuguese winger was sent on just before halftime in place of the injured Phil Jones and he scored United's opener before setting up Javier Hernandez for the second.
The Premier League leaders dominated the match but struggled to make the breakthrough in the face of resolute Reading defending and a fine performance by goalkeeper Adam Federici.
Nani, linked with a move away from Old Trafford, grabbed the first with a cute volley from 12 metres after 69 minutes and his pinpoint cross set up Hernandez for a trademark near-post header soon afterwards.
Reading refused to lie down and Jobi McAnuff pulled one back nine minutes from time with a neat finish from close range.
The side third-bottom of the Premier League table continued to press forward but the hosts, bolstered by the reassuring presence of experienced Serbian Nemanja Vidic at the heart of their defence, hung on.
United, record 11-time FA Cup winners but who have not lifted the trophy since 2004, will play second-tier Middlesbrough or European champions Chelsea in the quarterfinals.
