Brighton were unlucky to lose 3-2 after a thrilling Premier League encounter packed with controversial incidents.
Neal Maupay gave the home side the lead from the penalty spot but United were level just 194 seconds later when Brighton captain Lewis Dunk knocked the ball into his own net following a free-kick.
Brighton thought they had been given another spot-kick early in the second half when Paul Pogba appeared to trip Aaron Connolly – but referee Chris Kavanagh reversed his decision after watching the incident on the pitchside monitor.
"Connolly did everything right there," Shearer said speaking on Match of the Day. "As a forward you are taught to do that which is get across the defender and make him foul you and that's exactly what he did.
"When the referee gave the penalty I was amazed that he thought it was a clear and obvious error by looking at the monitor to go against his original decision."
"Connolly was brilliant today," added Micah Richards. "Running in behind and he gave United all sorts of problems. There is a touch from Pogba. Just his left left leg onto his right leg and a tug of the shirt. For me that was a penalty."
Marcus Rashford soon mad it 2-1 to the visitors when he collected the ball on the left, powered into the penalty are and danced around the Brighton defenders to fire United in front on 55 minutes.
Brighton were denied twice more by efforts hitting the woodwork before Solly March finally nodded in an equaliser during the fifth minute of added time.
There was, however, more late drama to come after Harry Maguire headed against the outstretched arm of Maupay.
Players from both teams surrounded match official Kavanagh, who had initially blown for full-time only for VAR to indicate a penalty.
Portugal international Fernandes kept his cool to lash the spot-kick.
"Brighton were unfortunate but poor finishing has cost them," Shearer said of Brighton who the woodwork an incredible five times during the match. "There is no way they deserved to lose that game.
"Brighton ran them ragged defensively. The space that United allowed Brighton was incredible."