Javier Garrido came close to breaking the deadlock with an early effort before Robin van Persie spurned a chance to put United ahead in the 40th minute.
Chris Hughton’s side, who are now in 13th place in the Premier League, took the lead with 30 minutes remaining courtesy of Pilkington’s header after good work by Garrido.
“You’ve got to give credit to the way Norwich defended – they defended for their lives,” said Ferguson.
“The only chances we had were half chances. Their goalkeeper had a good night too. We had a lot of pressure but didn’t get the goal we needed.”
Meanwhile, Norwich’s match-winner Pilkington heaped praise on his team-mates for producing a great performance to beat the 19-time English champions.
“It’s a great day for the fans and Norwich City,” said Pilkington.
“We’ve got a great squad here and a great set of players. The management said ‘keep believing’ – that’s what we’ve done. Now we’re unbeaten in the last six games and we’re starting to beat teams.
“It’s never over until it’s over against Manchester United. They score goals in the 95th and 96th minutes and it’s hard going. But we managed to hold on and get the win.”