Two proofs: (thanks for Julien for helping me fix the first proof)
First proof:
First assume $A,B>0$. Suppose $B \geq A$.
$$B-A \geq 0 \\ A^{-1/2}BA^{-1/2} - I \geq 0, $$
since $M\geq 0 \Rightarrow N^{*}MN \geq 0$ for $N$ invertible. This means all eigenvalues of $A^{-1/2}BA^{-1/2}$ are strictly greater than 1. Therefore for all $\|x\|=1$
$$\langle A^{-1/2}BA^{-1/2}x,x \rangle \geq 1 \\ \langle BA^{-1/2}x, A^{-1/2}x \rangle \geq 1 \\ \langle B^{1/2}A^{-1/2}x, B^{1/2}A^{-1/2}x \rangle = \|B^{1/2}A^{-1/2} x\|^2\geq1 \\ \|B^{1/2}A^{-1/2} x\|\geq1$$
so all eigenvalues of $B^{1/2}A^{-1/2}$ are strictly greater than 1 in modulus. But by a similarity transformation, these are also the eigenvalues of $A^{-1/4}B^{1/2}A^{-1/4}$, and those are all positive since $A^{-1/4}B^{1/2}A^{-1/4}$ is positive (being of the form $N^* M N$ for $M>0$ and $N$ invertible). So
$$A^{-1/4}B^{1/2}A^{-1/4}-I \geq0\\B^{1/2}-A^{1/2}\geq0,$$
finishing the case $A,B>0$. To extend to $A,B\geq 0$, let $A_\epsilon:=A+\epsilon I$, and similarly for $B_\epsilon$. Then $B\geq A \Rightarrow B_\epsilon \geq A_\epsilon \Rightarrow (B_\epsilon)^{1/2}\geq (A_{\epsilon})^{1/2} \Rightarrow B^{1/2}\geq A^{1/2}$, if you believe that $\epsilon \mapsto M_\epsilon^{1/2}-N_{\epsilon}^{1/2}$ is right-continuous in the eigenvalues at zero (follows from $\epsilon \mapsto M_\epsilon^{1/2}$ being right-continuous in the eigenvalues).
Second Proof (from Lax's book Linear Algebra and its Applications): This relies on the fact that if $A(t)$ is a matrix-valued function whose derivative is everywhere positive definite, then $t_2 > t_1 \Rightarrow A(t_2) > A(t_1)$ (unstrict inequality corresponds to positive semidefiniteness). Also it uses the lemma that if $A$ is positive definite and $AB+BA$ is positive definite, then $B$ is positive definite. And it uses that positive semidefinite matrices are a convex subset of $\mathbb{C}^{n^2}$ (all these proofs can be found in Lax's book in the section on matrix inequalities).
Let $B\geq A \geq 0$. Define a function $M(t) = A + t(B-A)$. It is positive on $[0,1]$ by convexity (as a matter of fact, it is positive for all $t\geq0$, I believe). Further, it has a positive semidefinite matrix as its derivative. Also $\sqrt{M(t)}$ is positive semidefinite. Define $R(t) = \sqrt{M(t)}$. Then $R^2 = M$, so
$$R\dot{R} + \dot{R} R = M'(t) \geq 0.$$
$R$ is positive and $R\dot{R} + \dot{R} R$ is positive, so $\dot{R}$ is positive. Therefore $R$ is a non-decreasing function of $t$ and $R(1) \geq R(0)$. QED