Split up the integral by considering the domain in $xt$ space. The figure below considers $f(u)=\frac{1}{2} u^2$.
The location of the rarefaction wave trailing edge is defined by $x=f'(u_l)t$, and the leading edge is defined by $x=f'(u_r)t$. The left side of eq. 1 can be written
\begin{align*}
\int_0^\infty \int_{-\infty}^\infty\left[\phi_t u +\phi_x f(u)\right]dxdt
&= \int_{-\infty}^\infty \int_0^\infty\phi_t u~dtdx+\int_0^\infty\int_{-\infty}^\infty\phi_x f(u) dx dt\\
&=I_t+I_x
\end{align*}
First consider $I_t=\int_{-\infty}^\infty \int_0^\infty\phi_t u~dtdx$.
\begin{align*}
I_t&=\int_{-\infty}^\infty \int_0^\infty\phi_t u~dtdx\\
&=\int_{-\infty}^0 \int_0^\infty\phi_t u_l~dtdx+\int_{-\infty}^\infty \int_0^\infty\phi_t u~dtdx\\
&=\int_{-\infty}^0 -\phi(x,0)u_ldx\\&~~~~~+\int_{0}^\infty\left[\int_0^{x/f'(u_r)} \phi_t u_r~dt+\int_{x/f'(u_r)}^{x/f'(u_l)} \phi_t v(x/t)~dt+\int_{x/f'(u_l)}^\infty \phi_t u_l~dt\right]dx
\end{align*}
where we have used $\phi\in C_0^1(\mathbb{R}\times \mathbb{R}^+)$ to assert that $\phi(\infty,0)=0$.
Then, for convenience, define the following
\begin{align*}
I_{tl}&=\int_{x/f'(u_l)}^\infty \phi_t u_l ~ dt=-\phi(x,x/f'(u_l))u_l\\
I_{tm}&=\int_{x/f'(u_r)}^{x/f'(u_l)} \phi_t v(x/t)dt\\
I_{tr}&=\int_0^{x/f'(u_r)}\phi_t u_r~dt=\phi(x,x/f'(u_r))u_r-\phi(x,0)u_r
\end{align*}
Now consider $I_x=\int_0^\infty\int_{-\infty}^\infty\phi_x f(u) dx dt$.
\begin{align*}
I_x&=\int_0^\infty\int_{-\infty}^\infty\phi_x f(u) dx dt\\
&=\int_0^\infty\left[\int_{-\infty}^{f'(u_l)t}\phi_x f(u_l) dx+\int_{f'(u_l)t}^{f'(u_r)t}\phi_x f(v(x/t)) dx+\int_{f'(u_r)t}^{\infty}\phi_x f(u_r) dx\right]dt
\end{align*}
So
\begin{align*}
I_{xl}&=\int_{-\infty}^{f'(u_l)t}\phi_x f(u_l) dx=\phi(f'(u_l)t,t)f(u_l)\\
I_{xm}&=\int_{f'(u_l)t}^{f'(u_r)t}\phi_x f(v(x/t)) dx\\
I_{xr}&=\int_{f'(u_r)t}^{\infty}\phi_x f(u_r) dx=-\phi(f'(u_r)t,t)f(u_r)
\end{align*}
Now apply integration by parts to $I_{tm}$ and $I_{xm}$. Then
\begin{align*}
I_{tm} &=\int_{x/f'(u_r)}^{x/f'(u_l)} \phi_t v(x/t)dt\\
&=\phi v(x/t)\big|_{t=x/f'(u_r)}^{t=x/f'(u_l)}-\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)(-\frac{x}{t^2})dt\\
&=\phi(x,x/f'(u_l))v(f'(u_l))-\phi(x,x/f'(u_r))v(f'(u_r))+\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)\frac{x}{t^2}dt\\
&=\phi(x,x/f'(u_l))u_l-\phi(x,x/f'(u_r))u_r+\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)\frac{x}{t^2}dt
\end{align*}
where $v(f'(\nu))=\nu$ by the definition of $v$ as the inverse of $f'$. (Note, by the assumed convexity of $f(u)$, its inverse exists.)
\begin{align*}
I_{xm} &=\int_{f'(u_l)t}^{f'(u_r)t}\phi_x f(v(x/t)) dx\\
&=\left.\phi f(v(x/t))\right.\vert_{x=f'(u_l)t}^{x=f'(u_r)t}-\int_{f'(u_l)t}^{f'(u_r)t}\phi f'(v(x/t))v'(x/t)\frac{1}{t}dx\\
&=\phi(f'(u_r)t,t)f(v(f'(u_r)))-\phi(f'(u_l)t,t)f(v(f'(u_l)))-\int_{f'(u_l)t}^{f'(u_r)t}\phi v'(x/t)\frac{x}{t^2}dx\\
&=\phi(f'(u_r)t,t)f(u_r)-\phi(f'(u_l)t,t)f(u_l)-\int_{f'(u_l)t}^{f'(u_r)t}\phi v'(x/t)\frac{x}{t^2}dx
\end{align*}
where $f(v(f'(u_r)))=f(u_r)$ by the definition of $v$ as the inverse of $f'$.
Let's summarize what we have.
\begin{align*}
\int_0^\infty \int_{-\infty}^\infty\left[\phi_t u +\phi_x f(u)\right]dxdt &= I_t+I_x\\
&= \int_{-\infty}^0 -\phi(x,0)u_l dx+ \int_0^\infty \left[ I_{tl}+I_{tm}+I_{tr} \right]dx+\int_0^\infty\left[I_{xl}+I_{xm}+I_{xr}\right]dt
\end{align*}
Looking at the results for each of these integrals, we might hope that everything will cancel nicely with an appropriate substitution. Consider $\int_0^\infty I_{tl} dx$ and $\int_0^\infty I_{xl} dt$. For the $I_{tl}$ integral, let $w=x/f'(u_l)$, so $f'(u_l)dw=dx$.
\begin{align*}
\int_0^\infty I_{tl} dx &= -\int_0^\infty \phi(x,x/f'(u_l))u_l~dx\\
&= -\int_0^\infty \phi(f'(u_l)w,w)f'(u_l)u_ldw\\
\int_0^\infty I_{xl} dt &= \int_0^\infty \phi(f'(u_l)t,t)f(u_l)~dt
\end{align*}
Not quite cancellation, but maybe we can work with it.
$$
\int_0^\infty I_{tl}~dx+\int_0^\infty I_{xl}~dt=(f(u_l)-f'(u_l)u_l)\int_0^\infty \phi(f'(u_l)w,w)~dw
$$
Similarly, consider $\int_0^\infty I_{tr}~dx$ and $\int_0^\infty I_{xr}~dt$. Let $w=x/f'(u_r)$, so $f'(u_r)dw=dx$.
\begin{align*}
\int_0^\infty I_{tr}~dx &= \int_0^\infty \phi(x,x/f'(u_r))u_r~dx-\int_0^\infty\phi(x,0)u_r~dx\\
&= \int_0^\infty \phi(f'(u_r)w,w)f'(u_r)u_r~dw -\int_0^\infty\phi(x,0)u_r~dx\\
\int_0^\infty I_{xr}~dt &= -\int_0^\infty \phi(f'(u_r)t,t)f(u_r)~dt
\end{align*}
So
$$
\int_0^\infty I_{tr}~dx +\int_0^\infty I_{xr}~dt = (f'(u_r)u_r-f(u_r))\int_0^\infty \phi(f'(u_r)w,w)~dw - \int_0^\infty \phi(x,0)u_r~dx
$$
Now consider $I_{tm}$ and $I_{xm}$. Again, make the substitution $w=x/f'(u_*)$.
\begin{align*}
\int_0^\infty I_{tm}~dx&=\int_0^\infty\left[\phi(x,x/f'(u_l))u_l-\phi(x,x/f'(u_r))u_r+\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)\frac{x}{t^2}dt\right]~dx\\
&=\int_0^\infty\left[\phi(f'(u_l)w,w)f'(u_l)u_l-\phi(f'(u_r)w,w)f'(u_r)u_r\right]dw+\int_0^\infty\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)\frac{x}{t^2}~dtdx\\
\int_0^\infty I_{xm}~dt&=\int_0^\infty\left[\phi(f'(u_r)w,w)f(u_r)-\phi(f'(u_l)w,w)f(u_l)\right]dw-\int_0^\infty\int_{f'(u_l)t}^{f'(u_r)t}\phi v'(x/t)\frac{x}{t^2}~dxdt
\end{align*}
Note that
\begin{align*}
\int_0^\infty I_{tm}~dx+\int_0^\infty I_{xm}~dt
&= (f(u_r)-f'(u_r)u_r)\int_0^\infty \phi(f'(u_r)w,w)~dw\\
&+(f'(u_l)u_l-f(u_l))\int_0^\infty \phi(f'(u_l)w,w)~dw\\
&+\int_0^\infty\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)\frac{x}{t^2}~dtdx-\int_0^\infty\int_{f'(u_l)t}^{f'(u_r)t}\phi v'(x/t)\frac{x}{t^2}~dxdt
\end{align*}
I claim that
$$
\int_0^\infty\int_{x/f'(u_r)}^{x/f'(u_l)}\phi v'(x/t)\frac{x}{t^2}~dtdx=\int_0^\infty\int_{f'(u_l)t}^{f'(u_r)t}\phi v'(x/t)\frac{x}{t^2}~dxdt
$$
Both of these integrals have the integrand $\phi(x,t)v'(x/t)x/t^2$ and are over the region between the trailing and leading edge of the rarefaction wave in $xt$ space. By Fubini's theorem, they are equal.
Finally, by examining all of the integrals computed so far, we can see that
\begin{align*}
\int_0^\infty \int_{-\infty}^\infty\left[\phi_t u +\phi_x f(u)\right]dxdt &= I_t+I_x\\
&= \int_{-\infty}^0 -\phi(x,0)u_l dx+ \int_0^\infty \left[ I_{tl}+I_{tm}+I_{tr} \right]dx+\int_0^\infty\left[I_{xl}+I_{xm}+I_{xr}\right]dt\\
&=-\int_{-\infty}^0 \phi(x,0)u_l~dx-\int_0^\infty \phi(x,0)u_r~dx\\
&=-\int_{-\infty}^\infty \phi(x,0)u(x,0)~dx
\end{align*}
which is precisely what we wanted to show.