Manchester United's dream of emulating the 1999 treble-winning team is still alive. The target remains distant but they are now safely into an FA Cup quarter-final against Chelsea or Middlesbrough.

Asked about the prospect of again claiming the title, Cup and Champions League Sir Alex Ferguson said: "Tonight was a tie we got out of the road and now we have a big league game on Saturday at QPR and hopefully we can keep the momentum going."

The one sour note for United was the sight of Phil Jones limping off before half-time. He was later seen leaving on crutches and Ferguson said: "We will have to assess it in the morning. It is an ankle injury so I would imagine he would not be ready for Saturday and we will see what he is like after that."

United wobbled late on when Jobi McAnuff was quicker than Alexander Büttner to a rebound to pull a goal back for Reading inside the last 10 minutes but they survived.

The visitors had got to 68 minutes with the game scoreless before Nani settled home nerves. He completed neat work from Antonio Valencia, who threaded a short pass to him inside Reading's area. After the ball had flipped up on Nani's left boot the winger volleyed home with the other to make it 1-0.

Before Javier Hernández scored what proved to be the winner David De Gea was called upon to retain United's advantage with a sharp save to stop Adam Le Fondre's attempt from a few yards out.

The Mexican's 15th of the season was created by Nani, who begun the evening on the bench. He flew down the right then zipped over a cross which Hernández headed home sweetly. "We were struggling in the last few minutes because Reading really went for it but we were able to hang on. Nani was brilliant today," the striker said.

Ferguson made eight changes for this tie. Only Jones, De Gea and Danny Welbeck remained from the side that drew 1-1 at Real Madrid last time out in the Champions League. The XI sent out to face Brian McDermott's band featured Nemanja Vidic, whose knee was not deemed worth risking at the Bernabéu. Twice during the first half the captain was called upon to clear awkward corners that were dipped in from Nicky Shorey's left boot.

Each time Vidic, who required treatment for an eye wound early on, stuck his head in to ensure a danger that had been Reading's main ploy when these sides met on 1 December was repelled.

That game was a chaotic league encounter which featured a seven-goal glut in the opening 34 minutes of which United emerged, relieved, on the right side of a 4-3 win. All of Reading's strikes came from high balls that Anders Lindegaard and his defence could not handle and following his part in the display the Danish keeper has been selected only once by Ferguson.

As the sides wandered off at half-time United may have expected a stern word from the Scot to up the tempo and use their superior technical ability to apply the killer touch. They had created a crop of chances but had no one to finish them. On 21 minutes Tom Cleverley blazed at Adam Federici who saved well, then Ashley Young's follow-up was blocked for a corner. Before this Hernández, the lone striker in United's 4-2-3-1 formation, had danced into Reading's area before shooting and when the ball came to Antonio Valencia a weak header looped into Federici's hands.

Nani came closest. On as a replacement on 43 minutes for Jones following his clash with McAnuff, he belted a volley that beat Federici but not his right post. Then a corner was forced with a swinging left-foot effort.

Robin van Persie's entrance as a 64th-minute substitute for Young injected urgency into United with Anderson feeding a Hernández run, with Nani this time winning a corner. After the two goals, United survived Reading's late rally with McDermott saying: "I thought we might nick a draw at least – we gave them a real run for their money."

The murmur around United about winning a second treble has been audible recently. Players, fans and pundits have all begun speaking of a repeat of the feat achieved by Dwight Yorke, Roy Keane, Ryan Giggs, David Beckham and co.

Ferguson, who was without Wayne Rooney because of a sinus infection, said he is just focusing on keeping the Cup run going. "We have a home tie and it can't get any better than that," he said. "No matter who we play, a home tie at Old Trafford means we have a great chance."