Dutschke was shot three times by a right-wing fanatic on April 11, 1968 while leaning on his bicycle outside a pharmacy on West Berlin's Kurfürstendamm where he wanted to buy medicine for his baby son.
He survived but never fully recovered from the injuries and died in Denmark in 1979 after suffering an epileptic seizure.
Among those who visited the scene of the shooting Friday was his American widow Gretchen Klotz-Dutschke.
"Today we remember the assassination attempt on Rudi Dutschke but also the many other people who died because they tried to make the world a better place," she said.
Dutschke was born in the former East Germany and fled to the West with his family in 1961 just before the Berlin Wall was built.
By 1968 he had become the emblematic frontman of the left-wing student movement, and pleaded for the youth to seek to reform state institutions from within.
The attempt to kill him followed a hate campaign whipped up by the conservative tabloids, in particular the top-selling Bild daily newspaper with its calls to "Stop Dutschke Now."
Dutschke remains a controversial figure in Germany. Plans to name a street in Berlin after him have sparked a protracted debate.