"I had already told the BBC I would extend my contract with them. I didn't want to break my word," Shearer said to the Football Association's website.
Shearer was approached by McClaren prior to the World Cup, but has decided to stay on in his current role as a pundit for BBC media.
"I fully understand the reasons behind Alan's decision. He is a top professional and a great guy," new team manager McClaren said.
The 35-year-old former England captain retired from professional football at the end of last season, and chose to take a break from the high pressure sport.
"I also want some time away from the pressures of football - I am currently on my longest ever family holiday and enjoying every minute of it," Shearer said.
While McClaren understood Shearer's decision, he was quick to lament his inability to woo the football legend.
"I would have loved to have had him on board," McClaren said.
"But as you would expect from Alan he has chosen to honor a contract to which he had verbally committed - a true mark of the man."