Judges Ola and James Jordan and Ade Adepitan chose the pair over Olympic swimmer Mark Foster and Diana Morgan-Hill. Flack and O'Shea will now represent the UK at the wheelchair dancing European Championships in Tel Aviv, Israel.
"You've reached an excellent level of dancing in a short space of time and we think both couples would do a great job of representing us at the European Championships," said Strictly Come Dancing star James before the result was announced.
"If I could, I would send both of you to the European Championships," added Ola.
Brian Fortuna, who trained the couples on the show, said: "I'm very proud of James and Caroline. They have achieved a great accomplishment. But they have got to work amazingly hard now to keep on a par with the rest of the European Championships."
"I cannot believe that me and James have won!" added Flack. "We now have a great responsibility to represent the UK. No more mucking around. We're serious dancers now."