The former Magpies captain is worried that Roberto Di Matteo's men will steal his old club's European thunder by beating Bayern Munich to snatch the fourth qualification spot
The Magpies currently sit fourth in the table, three points clear of Tottenham and four ahead of Chelsea with four games to play.
But should Chelsea beat Bayern Munich in next month’s final, the Blues will take the final Champions League spot regardless of their Premier League position - forcing the fourth-placed club into the Europa League.
Shearer told The Chronicle: "It's amazing what Newcastle have done. I hope I am wrong, but it would be just Newcastle's luck to finish fourth and Chelsea go and win the Champions League.
"I obviously want Newcastle to finish fourth, but I would also like Chelsea to go on and win the Champions League after the season they have had - not if it's at Newcastle's expense of qualifying for the Champions League though.
"It's a tough scenario."
The former England captain also hailed the contribution of Senegalese forwards Papiss Cisse and Demba Ba in propelling Newcastle up the league.
He said: "It's been an incredible season. It's worked out well for Papiss Cisse since he arrived.
"Demba Ba has stopped scoring goals and done an incredible job for the team, so Cisse has come in and started to score the goals. He has taken that on from where Ba left off.
"I hope Newcastle can finish the season off in style with Cisse scoring goals and getting them up to fourth."