Sir Alex Ferguson said he wanted to see his striker find the back of the net more often and Rooney responded with two strikes in a thrilling match at the Madejski Stadium, where all seven goals came in a 34-minute spell in the first half.
Hal Robson-Kanu gave Reading an early lead before United hit back with Anderson levelling and Rooney putting them ahead from the spot.
Reading stunned the visitors with two quick-fire goals to regain the lead as Adam Le Fondre and Sean Morrison capitalised on lapses in United's defence to both score with close-range headers.
But another effort from Rooney and a neat finish from Robin van Persie saw United take the spoils.
The second half was less entertaining but both sides still created decent chances on a day where neither team's defending was deserving of praise.
The home side went ahead in the seventh minute after Jonny Evans could only head Jobi McAnuff's cross into the path of Robson-Kanu, who volleyed past Anders Lindegaard.
United found themselves in the familiar position of chasing a game and soon showed their ruthlessness when coming from behind.
Anderson picked out Ashley Young wide on the left and the Brazil international continued his run before Young picked him out and he lashed United level.
Just nine minutes after falling behind the visitors were ahead after Jay Tabb bundled into the back of E
Reading were level just three minutes later as United fan Le Fondre wriggled free of Evans in the area to head home a Nicky Shorey corner.
Brian McDermott's side have shown great resolve this season and took advantage of further poor defending from United to re-take the lead.
Moments after Rio Ferdinand had headed away a cross ta the back post, Morrison beat Evans to a corner and powered a close-range header past Lindegaard.
With title rivals Manchester City being held at home to Everton earlier in the day, United knew a win was vital ahead of the Manchester derby next weekend and they were soon back on top.
A sublime piece of skill from Young freed Patrice Evra down the left and his low cross was tucked away by Rooney to make it 3-3 with only half an hour gone.
Ferguson decided to make a tactical substitution and replaced Rafael, who had been cautioned moments earlier, with the more powerful Chris Smalling, although the Brazilian did not take kindly to being hauled off.
Just four minutes after Rooney's effort United took the lead yet again.
Michael Carrick's through-ball was deflected into the path of Van Persie by a clever Rooney touch and the Dutchman slotted past Federici with his weaker right foot.
United were denied a fifth goal before half-time as Van Persie pounced on a smart Federici save and directed an effort goalwards. Adrian Mariappa was in the right place to clear but it appeared the whole of the ball had crossed the line before the former Watford man hacked it away.
The second half started much calmer but it was the home side who were pressing forward.
Lindegaard fumbled a simple catch from a Shorey corner before Halsey waved away Reading appeals for a penalty after Evra won the ball in a challenge with Mariappa.
Van Persie wasted a good chance to put United two clear when he shot wide after being picked out by Phil Jones, although the ball into the ex-Arsenal striker was slightly behind him.
The 29-year-old missed an even better opportunity moments later as he robbed the ball off a dallying Federici but could not hit the empty net from a relatively tight angle.
McDermott introduced Pavel Pogrebnyak for the tiring Jason Roberts as his side went in search of an equaliser.
Smalling found himself in space on the right flank with just three minutes left on the clock but he could only blaze an uncontrolled effort into the United fans behind Federici's goal.
Reading pushed on in stoppage time and a Morrison header was tipped over by Lindegaard with the same player heading wide from the resulting corner as United just held on.
Source: PA
Source: PA