The right-wing documentary, which one critic described as an "embarrassment to propaganda films", took home raspberry-shaped trophies for "Worst Picture", "Worst Director", "Worst Actor" (for D'Souza, who plays himself, in dramatized parts) and "Worst Actress" (for breakout Becky Turner, who played Hillary Clinton).
They said: "The crop of cinematic crap in 2016 was so extensive that this year's 37th annual Razzie Awards is expanding the number of nominees from the usual five to an unprecedented six contenders in each of its nine worst achievement in film categories".
But the clear winners - or losers - on the night were Batman vs. Superman: Dawn of Justice, which claimed four Razzies, and documentary Hillary's America: The Secret History of the Democratic Party.
It might not have picked up many Oscar nominations, but there's one awards ceremony which has honoured Batman v Superman - although not necessarily the one you might want to win.
D'Souza was a good sport about it and appeared in the video announcement of the winners.
The 2017 Golden Raspberry awards, to give them their official title, follow a Hollywood awards season marked by outspoken speeches and protests against the policies and behavior of President Donald Trump.
"Batman v Superman" took home Razzies for worst screen combo for "Ben Affleck & His BFF (Baddest Foe Forever) Henry Cavill" and worst "remake, rip-off or sequel".
In a recorded message, D'Souza thanked the academy for the prizes, saying: "Being dissed by you guys, this is absolutely fantastic". "My audience loves the fact that you hate me!"
"You've never got over it, you probably never will".
The only two remaining awards went to Kristen Wiig-for her supporting role in Zoolander 2-and Mel Gibson, who earned a special "redeemer" award.
The 37th Annual Razzie winners were announced on February 25 in line with tradition of sharing the performances that bombed just one day before the actual Academy Awards.