In order to avoid that "small intermission" or slight interruption between iterations, the signal must have a smoothly varying phase across the iteration transition. In this case, that can be done by constructing your signal with one fewer sample at the end so that you're not repeating that sample when the next sound starts:
Fs = 44100; % Sample rate (samples per second)
duration = 3; % Duration of each tone in seconds
frequency = 440; % Frequency of the tone in Hz
% t = 0:1/Fs:duration;
t = (0:duration*Fs-1)/Fs; % one fewer sample at the end
tone = sin(2*pi*frequency*t);
while true
sound(tone, Fs);
pause(duration) % (use the duration variable instead of hard-coding 3)
end
