His side currently sit fifth in Group C after their defeat to Serbia on Friday, but although they are 10 points behind leaders Italy, they sit only two behind second-placed Slovenia.
"It is difficult now but we have to stay positive," he said. "There's no point carrying on otherwise.
"We have three games to go and we've got to believe we can do it. I am gutted for everybody about what happened against Serbia but we have to get the players back up and get them going again. Estonia will be a very tough game but there is still a lot to play for."
Worthington has had to draft in Andrew Little and Josh Carson for Tuesday's game in Tallinn after brothers Corry and Jonny Evans both picked up suspensions for the match.