This is false in general. For example if $B=\mathbb Z/p\mathbb Z$ and $A=\mathbb Z$, then certainly $B$ is a finitely generated $A$-module, but $\mathbb F_p$ is not even a field extension of $\mathbb Q$. Alternatively, if $A=\mathbb Z[X]$, $B=\mathbb Z$ and $\varphi: f(X)\mapsto f(0)$, then $F_1$ is isomorphic to an infinite extension of $F_2$.
However, this is true if $\varphi$ is injective, in which case we can view $A$ as a subring of $B$.
Indeed, pick a set of generators $x_1,\ldots, x_n\in B$ of $B$ as an $A$-module. It follows that $F_2 = F_1(x_1,\ldots, x_n)$.
Indeed:
- Clearly $F_1(x_1,\ldots, x_n)\subset F_2$, since $F_1\subset F_2$ and $x_1,\ldots, x_n\in B\subset F_2$.
- Conversely, if $y\in F_2$ is non-zero, then there exists a non-zero $b\in B$ such that $by\in B$. Since $b$ and $by$ can both be expressed as $A$-linear combinations of the $x_i$, it follows that $b,by\in F_1(x_1,\ldots,x_n)$. Since $F_1(x_1,\ldots,x_n)$ is a field, it follows that $y\in F_1(x_1,\ldots,x_n)$.
It remains to check that each $x_i$ is algebraic over $F_1$. This is clear, since if $1,x_i,x_i^2,\ldots$ were linearly independent over $F_1$, they would also be linearly independent over $A$, which would contradict the fact that $B$ is finitely generated.