"We are massively disappointed," Di Matteo said after the match at Stadium MK on Friday night.
"It's been a long season and I thought we deserved to go through.
"We had a slow start but we finished the first half well and I thought in the second half we were brilliant.
"They have quality players in their team so it was always going to be difficult but we had chances to win the game.
"It's important the players are confident enough to take a penalty but we were in the driving seat after they missed. It's a real shame.
"The players have been fantastic this season, they have given me everything and in the end it just comes down to destiny."