The 10th-seeded Nalbandian was leading in the second set Sunday when he kicked the small barrier surrounding the line judge in anger. A piece of the barrier then hit the line judge, causing bleeding on his left shin.
After checking on the line judge, the chair umpire decided to end the match.
Nalbandian insisted he shouldn't have been disqualified.
"Sometimes you get very frustrated on court and it's tough to control that, and sometimes I do a mistake. So it's very tough to end a final like that," he said. "But sometimes we feel so much pressure from the ATP to play a lot of tournaments. They don't do anything (for) us, and today I do a mistake and I have to pay like that.
"I agree I do a mistake but sometimes everybody do a mistake and I didn't feel it had to end like that, especially in a final."
ATP rules state that any violent action will result in an automatic default.
"It's an unfortunate situation for everyone involved, the spectators, the tournament, the sponsors, the players and the linesman," Brad Drewett, ATP executive chairman and president, said in a statement. "David certainly did not mean for this to happen; however, the rules are very clear in a situation like this and causing injury to someone is an automatic default for any player."
Tournament director Chris Kermode said the unidentified line judge had received first-aid care but needed no further treatment after seeing a doctor.
"It's definitely not the way I wanted to win it," Cilic said. "The match was still open but I can't change it. I'm sorry for the (spectators) that it had to end like this.
"We had some good rallies, and it's hard to see the final end like this."
The Argentine had been leading the sixth-seeded Cilic 7-6 (3), 3-4 in the grass-court Wimbledon warm-up when the incident occurred.
"There is a lot of rules, and sometimes they (ATP officials) don't do anything. The rule book is very big and I can tell you that the ATP do a lot of mistakes to the players and nothing happens," Nalbandian said.
Nalbandian was playing his first final on grass since losing to Lleyton Hewitt at Wimbledon 10 years ago. He was bidding to become the first player from Argentina to capture an ATP grass court title since Javier Frana won at Nottingham in 1995.
Nalbandian's last title came in Washington in August 2010.
"We have a sold-out crowd. It's packed. We were watching some great tennis so to have the match end this way is incredibly disappointing," Kermode said. "In sport, these things happen. There's not a lot we can do about it. We are under the governorship of ATP rules and that's how it stands. It's a great crowd, great final. You'd like to think you can bend it, but I can see from their point of view it's difficult."