Yale catcher Darren Beasley and designated hitter Dave Fortenbaugh incited the rally with back-to-back singles.
Crockett then made an errant throw on a pick-off attempt, allowing the runners to move into scoring position.
A sacrifice bunt and an RBI-single by the next two batters gave Yale a 2-1 lead.
Harvard was able to tie the game in the third, as Shakir hit a one-out single that brought Llanes, who had doubled, around from second.
Yale, however, pounded out two more runs in the bottom of the third, putting the Bulldogs ahead to stay.
Yale reliever Jon Steitz (2-4) held Harvard scoreless over the next six innings, striking out nine en route to the win.
The Crimson did have a chance to tie the game in the fourth, as it had two runners in scoring position with just one out.
But Steitz got Harvard seniors Jeff Bridich and Eric Binkowski to strike out looking, stifling any chance for a potential rally.
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