The two sides battled to a 2-2 draw at Wembley before the Blues went on to win 4-1 in the shoot-out.
Nani opened the scoring for United in the 10th minute with a long-range effort across goal that evaded goalkeeper Petr Cech.
Ricardo Carvalho headed home the equaliser for Chelsea early in the second half before an effort from Frank Lampard gave the Londoners the lead.
Despite an injury-time leveller from Wayne Rooney, the United boss was disappointed that referee Foy played on in the build-up to Chelsea's second goal, with Patrice Evra lying down injured.
"I think the referee clearly saw it," Ferguson told Sky Sports.
"He's elbowed him in the face and he's clearly in line with the actual incident and I'm disappointed because he stopped the game twice before that for fouls, with players lying down.
"When Ballack was lying down he got up within seconds. He thought it was a serious foul but you've seen Ballack. That incident cost us the game really."
FrustrationManchester United dominated the early stages of proceedings at Wembley, but the Red Devils boss was frustrated at the way his side let Chelsea back in the game
He said: "We played well for a lot of the game and we should have put it to bed in the first half. Their first was a poor goal from our point of view, we should have defended it better but Chelsea at that point came into the game and were controlling it.
"The second goal as we saw shouldn't have been allowed but once they got that goal Chelsea weren't losing the game, I think they were in control, they got the equaliser and then penalty kicks - well we've never been that good at penalty kicks."
Asked whether he was concerned that some players feigned injury to get the game stopped, Ferguson said: "Well we've seen it time and time again.
"I don't think there's any question about that, but we've got to a level now where it's being used now as a professional way to get the game stopped."