The decision of the Football Association's council has been welcomed by Supporters Direct, which has also warned a change in legislation is required to prevent the idea being revisited.
"We welcome (the FA council's) recognition that Hull's name is intimately connected with the identity of the club," a spokesman for Supporters Direct said.
"However, this is not the end of the process. We have been consistent in saying that the FA must create a democratic, transparent process for consultation in matters such as these, and one that ensures that supporters have the final say on such matters through a binding vote."
There are no grounds for appealing the FA council's decision, but a further application could be made in 12 months' time.
An FA statement on Wednesday read: "The FA council has today rejected Hull City's application to change their playing name to Hull Tigers.
"The council's decision - carried by a 63.5 per cent vote of its members - came after a recommendation from The FA's membership committee.
"The council, which is made up of representatives from across football, fully considered the recommendation and the subsequent responses received from Hull City in reaching its decision."
The saga has rumbled on in the background of Hull's successful season which this weekend takes in an FA Cup semi-final against Sheffield United at Wembley.
A statement on hullcitytigers.com read: "The club will not be making any comment on the outcome of today's FA meeting.
"Our focus is on supporting Steve Bruce and the team ahead of Sunday's FA Cup Semi-Final, our first in over 80 years.
"We look forward to seeing you all at Wembley."
Ian Waterson of City Til We Die hopes Allam will abide by the decision.
He said: "As City Till We Die have said all along, we will respect the FA process and the decision and we hope the club has the good grace to do likewise.
"Quite what course of action he'll take because he can't change the name is a question for the owner. As supporters this is the end of the line for us."