Goodell made his comments Thursday during a conference call about 12 hours after the referees' union and league agreed on a tentative deal that will allow the regular officials to return beginning with Thursday night's Browns-Ravens game.
Goodell says: "Something like this, it's painful for everybody. Most importantly, it's painful for fans. We're sorry to have to put fans through that."
He added: "Sometimes you have to go through something like that in the short term for the right agreement for the long term."
The deal was struck two days after Seattle's chaotic last-second win over Green Bay in which the replacements missed a call.