It follows a level of criticism and scrutiny that even Rooney has never before endured in what has been the ultimate of goldfish bowl careers.
In a column for the Sun, Shearer, who called time on his own international career at the age of 30, made plain he is on Rooney's side and doesn't like seeing the Manchester United forward subjected to such treatment.
"Over the years I have been one of his greatest admirers and stood up for him when others were calling for him to be dropped," Shearer explained.
"But the scenario I wanted to avoid was the very one that played out on Saturday at Wembley. The fact that it came against Malta in what should have been a game we comfortably won by five or six made it all the worse."
England won the game against the European minnows by a score-line of just 2-0 and it was another laboured performance from Rooney, who is now expected to drop to the bench when the team faces Slovenia on Tuesday.
"I did not want to see our country's greatest ever goalscorer and one of the best players to grace our game booed while wearing the captain's armband at Wembley," Shearer continued.
I can't think of anything much worse than being turned on by the very fans whose dreams you have worked so hard to make a reality. Obviously his concern about retiring after the summer Euros debacle would have been that he was bowing out on such a low note."
Drawing on his own experience, Shearer offered, "I went after Euro 2000 (group stage exit) which hardly saw us return home to an open-top bus parade. But I knew, I could tell, that my body could simply no longer handle the rigours of international and club football anymore.
"You could argue I was being selfish and, yes, I did want to prolong my career with Newcastle. However, would it not have been more selfish to continue trying to do both to, most probably, the detriment of both."
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