We outline a somewhat clumsy induction proof.
Suppose the result holds for all pairs $(a,b)$ with $a\le k$, $b\le k$. We show the result holds for all $(a,b)$ with $a\le k+1$, $b\le k+1$.
So let $a\le k+1$, $b\le k+1$. If $a\le k$ and $b\le k$, we know the result holds. If $a=k+1$ and $b=k+1$, the result is easy to verify. So we can assume that $a=k+1$ and $b\le k$.
By your result, $\gcd(2^a-1,2^b-1)=\gcd(2^{a-b}-1, 2^b-1)$. By the induction assumption, this is $2^{\gcd(a-b,b)}-1$. But $\gcd(a-b,b)=\gcd(a,b)$ so we are finished.
A much nicer conceptual proof is to observe that the process of subtracting the smaller number from the bigger that you initiated is precisely the (original) Euclidean gcd algorithm, so after a number of iterations of your procedure our two numbers are each $2^{\gcd(a,b)}-1$. But that takes a fair bit of notation to write up formally.