The England star was handed an immediate debut by Magpies manager Eddie Howe - but was unable to help his new side progress as Joe Ironside grabbed the only goal of the game to help the U’s pull off a major upset.
After declaring the performance as “pathetic” in a short tweet in the aftermath of the game, Shearer expressed his disappointment at the reaction of some Magpies players at full-time in an interview with BBC Breakfast on Monday morning.
He said: “Wasn't it brilliant for the FA Cup? It was fantastic for Cambridge.
“They took four or five thousand fans to St James' Park on Saturday and you could tell they were having the time of their lives and why not after what everyone has gone through.
“They were the better team, they turned up, they were hungry, they went after Newcastle and they thoroughly deserved it. They thoroughly deserved to go through to the next round.
“Newcastle were hopeless. It was a really disappointing day if you're a Newcastle fan.
“I was really surprised and disappointed to see some of the players just walk off the pitch without acknowledging the superb support inside St James' Park.
“It was a very disappointing day for them, but great for Cambridge and brilliant for the FA Cup."
Meanwhile, Cambridge match-winner Ironside has revealed his delight at following in the footsteps of his boyhood hero Shearer in netting a winner at St James Park.
The former Kidderminster Harriers and Macclesfield Town striker converted from close range 11 minutes into the second-half as his goal - and an inspired display from goalkeeper Dimitar Mitov helped the visitors to their first ever win on Tyneside.
After the game, Ironside said: “I can't describe it, I am a bit lost for words, it panned out how I dreamed about it last night.
“I am proud of every single one of us.
“I have got to play here and it it stuff I dreamed of, Alan Shearer was my hero, I grew up idolising him - now I have scored the winner at St James' Park.
“It doesn't matter how they go in, it could have been that or a worldie, I don't care.
“We have all dug in together and it is a momentous day for the football club.”