The Spaniard's strike looked to have hit a crowd of bodies in front of the line at the start of the second half at Wembley Stadium.
However, the goal was given to put Chelsea 2-0 ahead.
"I thought Mata's strike hit me and didn't go over, but the linesman's seen it and given it," Terry told BBC Sport. "I honestly don't think it went over the line but the linesman gave it and there's nothing we can do about that.
"Spurs are one of the best sides in the league. It was a great performance and a great result."
Roberto Di Matteo's side will now face Liverpool in the final at Wembley Stadium on Saturday, May 5.