The start to the match was marred by confusion when the coin had to be tossed twice after match referee Jeff Crowe failed to hear what Sangakkara had called.
But Vaughan wrote on his Twitter page that Sangakkara conned his Indian counterpart Mahendra Singh Dhoni.
"Sangakkara has stuffed Dhoni. He shouted tails in the first toss and lost it. You can hear it on air."
He later tweeted: "I hear tails shout at the toss.. Others hear heads... Inconclusive on the replays."
Vaughan went on to insist that the Sri Lankan skipper knew he had lost the toss the first time around.
"I think there was a bit of skulduggery at the toss. Kumar Sangakkara knew he'd lost that first toss, but he saw Dhoni hadn't really heard him!"