The home side were in the driving seat for most of the game and, with six minutes remaining, they led by nine points.
But a late rally by the men from the Erne county yielded a goal from the penalty spot by Sean Quigley plus four points, to make Clare manager Colm Collins sweat it out to the final whistle.
The Banner led 0-8 to 1-3 at the break and probably should have been further ahead but for some poor finishing up front.
Fermanagh grabbed their goal in the 15th minute when Quigley fisted a Conall Jones delivery to the net.
Clare’s win was ground out in the early part of the second half as they scored a goal and four to no reply inside 10 minutes.
Corner-forward Pat Burke hit the Fermanagh net in the 40th minute.
Despite that, it looked a foregone conclusion that Fermanagh were about to lose their first game of the league campaign until the late flourish.
But luckily for Clare, their opponents just came up short, on a day when Louth and Wexford were relegated.
P Burke (1-3); G Brennan (0-5 4f) S McGrath (0-4) J Malone (0-1), P Collins (0-1).
S Quigley (2-2, 1-0 pen 0-1f); D McQuade (0-2); D Kille (0-2); A Breen (0-1); C Jones (0-1); B Mulrone (0-1).
J Hayes, C Russell, K Harnett, M McMahon, S Hickey, G Kelly, D Ryan, G Brennan (Capt.) C O’Connor, S Collins, J Malone, S McGrath, S Brennan, P Collins, P Burke.
K Sexton for McMahon (49) B/C, E Coughlan for McGrath (65).
C Snow, M Jones, T Daly, N Cassidy, A Breen, R McCluskey, J McMahon, E Donnelly (Capt.), C Cullen, P McCusker, C Jones, B Mulrone, E McManus, S Quigley, C Flaherty.
E McHugh for Joenes (half-time), D Kelly for McMahon (half-time), D Kille for McManus ((49), D McQuade for Jones (52), R Lyons for Flaherty (61).
M Duffy (Sligo).