Richie Baker opened the scoring in the 53rd minute when he punished a ball watching James Keddy by racing onto a cross field pass and poking past Matt Gregg.
Soon afterwards, Bohemians supporters began throwing objects onto the pitch though Shelbourne immediately doubled their lead when Jason Byrne hammered home the second after being set up by Crowe.
Byrne ran to the Bohemians supporters to celebrate and earned a booking in the process though there were further coins and bottles thrown onto the pitch while several supporters had to be restrained.
When it all died down, Shelbourne remained in control and grabbed a third goal in the 65th minute when Crowe brilliantly lobbed Matt Gregg after beating the goalkeeper in a race for a long ball.
Bohemians: Gregg;
Shelbourne: Delaney; Heary, Hawkins, Rogers, Cahill; Moore (Baker 38), Ndo (Fleming 78), Crawford, Hoolahan; Crowe, Byrne (O Neill 74).