United were locked at 1-1 with the Magpies for over an hour, after Harry Maguire's header cancelled out Luke Shaw's own goal, but Bruno Fernandes - who had his 11th penalty for the club saved by Karl Darlow following 10 successful spot-kicks - eventually found the net from open play in the 86th minute.
Then the floodgates opened as Aaron Wan-Bissaka, with his first-ever goal in senior football - and Marcus Rashford followed up with emphatic finishes of their own to secure a comprehensive 4-1 away win at St. James' Park.
Bruce said, "They were a handful all night, some of their forward players and their movement we found it difficult. But you stay in it, they scored from a free kick we had and broke away and then towards the end we were a bit naive.
"Karl Darlow has been fantastic. He was brave when we needed him to be. You know your goalkeeper will have to play well against the big teams, I hope he will be OK next week [after picking up a knock].
"I thought we were a little bit too easy at times to play against. We will go away really, really disappointed because we were 10 minutes away and it could have gone either way when it gets that late.
"It is work in progress for us. We have tried to change and with that it will take time. The defeat looks worse than it really was."