The divestment is just the latest by Mr Gilbert, who co-founded Aberdeen in 1983.
Previous sales have been used to acquire a salmon beat on the River Dee in Aberdeenshire, as tax planning and to rebalance his portfolio.
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Mr Gilbert said: "Retiring is not in my DNA. I would like to work until I am 90.
"Just like Sir Alex Ferguson who is the longest serving manager in the Premier League, I'm one of the longest FTSE-100 chief executives."
At 58 years of age, Mr Gilbert is 13 years younger than Sir Alex.
Mr Gilbert sold 1,078,253 shares at 444p each on May 1, according to a stock market filing made by the company yesterday. This has left him with a holding of just 122,233 shares, worth £540,000.
However, he has awards totalling 2,248,492 shares from deferred bonus arrangements dating back six years which have reached their vesting dates. These have a market value of £9.9m.
Mr Gilbert could also receive 2,365,240 shares, worth another £10.4m, from deferred awards for 2010, 2011 and 2012 which will vest before December 2016.
Mr Gilbert's last sale of Aberdeen shares garnered him £4m in February. Since the summer of 2010 Mr Gilbert has sold a total of £18.3m of shares.
Mr Gilbert has benefited from a sharp rise in Aberdeen's share price as investors have flocked to its emerging markets and Asian equity portfolios.
Aberdeen's shares reached an all-time high of 458.7p this week after it pleased the City by increasing underlying first half profit by 37% to £222.8m.
Although its share price has since softened, Aberdeen closed yesterday at 448.1p, up 3.2p or 0.7% on the day.
Aberdeen's stock market worth stands at £5.4 billion.