Dos Santos, who scored his fifth goal in the tournament, broke the deadlock in the 88th minute to take Dynamos to 17 points and upto the fourth position in the league table.
A win in their last away encounter against Chennayin FC will be enough to take Dynamos to the knock-out stages while Pune at 16 points and in sixth place will now have to win their last game and look forward towards favourable results.
What makes his goal special was the move initiated from the right flank and Dos Santos again did all the spadework with his left-foot.
Alessandro del Piero got some 22 minutes of match time but didn't look like bothering the Pune defence.
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Pune should have got the equalizer in the dying moments when their Nigerian striker Dudu Omagbemi had a free header from a cross essayed by Saidou Panandetiguiri. But Dudu failed to direct his nod with Kristof Van Hout at his mercy.
Even Greek World Cup Kostas Katsouranis was guilty of not able to head home a perfect cross from Korean Park.