First of all, what would it even mean to push on the two-particle system (as opposed to pushing on each particle)?
That the external force acts on at least one of the particles in a scenario where the two particles "move together", with similar averaged acceleration, so the system can be ascribed one common average acceleration.
If the particles come apart, average accelerations of both particles are no longer similar and then the system is not moving as a whole.
For example, two oppositely charged particles can remain close to each other due to attractive forces that keep the particles orbiting each other.
Or some other, non-electromagnetic force can keep two or many more particles close to each other. For example, particles forming the negative charge on curved conductive surface of a solid body (e.g. a metal sphere) may remain put there despite their repulsion, because there are also forces of constraint due to the solid body, keeping the charged particles from jumping out and spreading out into non-conducting air/vacuum.
Second, if we could take care of the previous question, why does the two-particle system end up having more resistance to motion than each individual particle? How can we explain the change in inertia using forces and the EM field only?
In classical mechanics, even if the force acted directly on single particle only, that force would "feel it has to accelerate the other particle as well". More correctly, the effect of the external force on the particle it acts on (its acceleration) is smaller when the other particle is attached or keeps close to the first particle. The acceleration is as if the external force acted on a hypothetical particle with greater mass, equal to sum of masses of the particles. In EM theory, this rule - the force effect being as if there was a particle with mass that is sum of masses of the particles - is no longer necessarily true.
When a charged particle moves with non-zero acceleration, it produces dynamic electric field, one part of which is proportional to acceleration of the particle (cf. the terms in electric field in https://www.feynmanlectures.caltech.edu/II_21.html - the last term is proportional to particle's acceleration).
This "acceleration electric field" may act on other nearby charged particles. In inductors, it is responsible for the induced electric field and thus induced EMF pointing against the acceleration, thus adding more inertia to mobile charge carriers forming the current, and thus greater effective mass. This is because all the accelerating charges have the same charge sign, so the induced field is proportional to acceleration, but points in the opposite direction.
If there is just a pair of positive and negative charge, the same kind of acceleration field is present due to both particles, and acts on the other particle in direction of its acceleration, thus decreasing effective mass of both particles. This is the simplest system manifesting "electromagnetic mass effect", an increase or decrease of effective mass due to EM interaction in the system.