Rod Wallace had shot the Gills into a 10th minute lead but on loan star Luke Chadwick scored on his Royals debut to level matters on 13 minutes.
The home side pushed forward for a winning goal in the second period and were awarded a penalty in the 69th minute after goalkeeper Jason Brown brought down Nicky Forster.
Steve Sidwell stepped up but saw his effort saved by Brown.
However, The Royals kept going and Salako celebrated his birthday - he is 34 on Tuesday - in the best possible fashion with the winner two minutes from time.
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