If you are tired of reading the OP, just read this answer.
Easy-to-read illustration of the question
Let's first recap the steps in the question body by a sample simplex tableau.
\begin{align*}
\begin{array}{c|ccc|cc}
\small\text{basic var} & * & x_j & * & \overbrace{\small\text{RHS}}^{\text{current BFS: } \\ (y_{10},\dots,\color{blue}{y_{r0}},\dots,y_{n0})} & \small\text{ratio} \\ \hline
* & * & * & * & * & * \\
x_{s} & * & y_{sj} & * & y_{s0} & y_{s0}/y_{sj} \\
\vdots & \vdots & \vdots & \vdots & \vdots & \vdots \\
x_{t} & * & y_{tj} & * & y_{t0} & y_{t0}/y_{tj} \\
\vdots & \vdots & \vdots & \vdots & \vdots & \vdots \\
\color{blue}{x_r} & \color{blue}{*} & \color{blue}{y_{rj}} & \color{blue}{*} & \color{blue}{y_{r0}} & \color{blue}{\underbrace{y_{r0}/y_{rj}}_{\text{2. pick } least\ nonnegative\ ratio \\ x_r\ will \text{ be the leaving variable}}}\\
* & * & * & * & * & * \\ \hline
\small\text{obj fct row} & * & y_{0j} & * & \underbrace{y_{00}}_{\small\text{current obj fct val}} \\
& & \small{\text{1. pick } most\ negative \text{ number } y_{0j} \text{ here} \\ x_j\ will \text{ be the entering variable}}
\end{array}
\end{align*}
N.B. OP says that, in step 2, "the smallest positive element of that [the rightmost] column" is chosen. We are going to see that this is incorrect.
OP's problem
In step $\color{blue}{two}$, if there's a $\color{blue}{ratio\ y_{r0}/y_{rj} = 0}$, should we pick $\color{blue}{x_r}$ as the leaving variable? Or should we only pick $\color{blue}{postive\ ratios}$?
Answer
We should always choose the least nonnegative $\color{blue}{ratio}$, so if there's a row such that its $\color{blue}{ratio\ y_{r0}/y_{rj} = 0}$, we should pick it (or any other row of ratio 0).
Concrete example
This example is taken from an online LP notes.
\begin{array}{r|rrrrr|rr}
& x_1 & x_2 & x_3 & x_4 & x_5 & & \text{ratio} \\ \hline
x_3 & 0 & \bbox[border:1px solid]{2} & 1 & -1 & 0 & 4 & 2 \\
x_1 & 1 & 1/4 & 0 & 1/4 & 0 & 2 & 8 \\
x_5 & 0 & 1 & 0 & -1 & 1 & 0 & 0 \\ \hline
& 0 & -1/2 & 0 & 1/2 & 0 & 4 &
\end{array}
If we follow the steps in the questions body, we will choose "the smallest positive element" 2 instead of 0 at the ratio column. After one pivot operation, we'll break the feasibility.
\begin{array}{r|rrrrr|rr}
& x_1 & x_2 & x_3 & x_4 & x_5 & \\ \hline
x_2 & 0 & 1 & 1/2 & -1/2 & 0 & 2 \\
x_1 & 1 & 0 & -1/8 & 3/8 & 0 & 3/2 \\
x_5 & 0 & 0 & -1/2 & -1/2 & 1 & -2 \\ \hline
& 0 & 0 & 1/4 & 1/4 & 0 & 5
\end{array}
So we have to choose the least nonnegative ratio in order to get an optimal solution.
\begin{array}{r|rrrrr|rr}
& x_1 & x_2 & x_3 & x_4 & x_5 & \\ \hline
x_3 & 0 & 0 & 1 & 1 & -2 & 4 \\
x_1 & 1 & 0 & 0 & 1/2 & -1/4 & 2 \\
x_2 & 0 & 1 & 0 & -1 & 1 & 0 \\ \hline
& 0 & 0 & 0 & 0 & 1/2 & 4
\end{array}
Theoretical justification
To justify this choice of ratio, first note that in the RHS $y_{i0} \ge 0 \forall i \in \{1,\dots,n\}$ since the current basic feasible solution (BFS) is nonnegative.
To describe the properties of a leaving variable, we denote $x_r$ as the leaving variable for the rest of this solution.
Before calculating the $\color{blue}{ratio\ y_{r0}/y_{rj}}$, we have to make sure that it's defined. Therefore, the ratio is calculated only when $y_{rj} > 0$ or $y_{r0} = 0$ with $y_{rj} \ne 0$. (If the pivot $y_{rj} < 0$, then the new BFS will have $y_{r0}/y_{rj} \le 0$ at one of its components. Unless $y_{r0} = 0$, we'll get a contradiction.)
We then proceed to the calculations for the new BFS. If $\color{blue}{y_{rj}}$ is chosen as a pivot, it's clear from the above tableau that the new RHS are
$$(\dots,
y_{s0} - \frac{y_{sj}}{\color{blue}{y_{rj}}}\color{blue}{y_{r0}},\dots,
y_{t0} - \frac{y_{tj}}{\color{blue}{y_{rj}}}\color{blue}{y_{r0}},\dots,
\color{blue}{\frac{y_{r0}}{y_{rj}}},\dots
)$$
Each component above is nonnegative due to feasibility. For any current non-leaving basic variable $x_s$
$$ y_{s0} - \frac{y_{sj}}{\color{blue}{y_{rj}}}\color{blue}{y_{r0}} \ge 0 \iff \frac{y_{s0}}{y_{sj}} \ge \frac{y_{r0}}{y_{rj}}\stackrel{(*)}\ge0.$$
Hence we should choose the least nonnegative ratio.
Note: (*) is true due to our choice of pivot element $y_{rj}$.