You don't need to measure the acceleration during the collision. For one thing, the force between the bodies (that is $F_{BA}$, the force that A exerts on B, and $F_{AB}$, the force that B exerts on A) will continuously change in magnitude during the collision, and so will the bodies' accelerations. But $F_{BA}=-F_{AB}$ at all times (N's Law 3) so, according to N's Law 2, $$\frac{dp_B}{dt}=-\frac{dp_A}{dt}.$$in which $p_A$ and $p_B$ are the momenta of A and B. This equation integrates up to give The Law of Conservation of Momentum applied to two bodies, namely$$p_{A}+p_{B}= \text{constant}.$$If the bodies start from rest and spring apart (a so-called 'explosive collision'), then we have$$p_{A}=-p_{B}\ \ \ \ \ \text{that is}\ \ \ \ \ m_{A}v_A=-m_{B}v_B$$in which $v_A$ and $v_B$ are the bodies' velocities as measured any time after the collision, even when the bodies are well separated – provided friction hasn't slowed them down.
So you can test the joint consequence of N's 2nd and 3rd laws for bodies of fixed mass, by showing that the ratio of their velocities after an explosive collision is constant. I don't think Newton could have done this with any precision, as he didn't have access to air-tracks and suchlike, so friction would have spoiled his experiments. [That's yet another mark of Newton's genius: he was able to figure out the laws of dynamics from how planets and satellites moved, and to realise that the same laws applied here on Earth – though he couldn't test them here anything like adequately.]
If you want to test N's 2nd law by itself you might pull a trolley by a single spring stretched to a known extension, then by two such springs stretched to the same extension, in parallel with each other and so on, measuring the acceleration each time. Friction compensation needed. Although it's possibly not beyond dispute that two identical, identically stretched springs in parallel will exert twice the force that a single one exerts, I find it very hard to doubt, as it's so closely bound up with my concept of force (a concept not wholly captured by "mass $\times$ acceleration" or "rate of change of momentum"). [Note that I'm not relying on Hooke's law.]
[The springs and trolley experiment was (and possibly still is) done in many schools in the UK to teach pupils in their mid teens about forces and Newton's laws. I believe it originated with the Nuffield science teaching initiative.]