The vent fitting on a tank is always on or at the top of the tank...so a tank that's nearly empty cannot be overflowing out the vent. If you think it is because you've recently pumped it out, the pumpout wasn't able to remove more than a gallon or two before a blocked vent caused the pump to pull a vacuum. The vent IS blocked...flushing the toilet is pressurizing it enough to force at least a little out the vent each time.
Holding Tank Vents 101: The vent on all tanks--water, fuel, waste holding--has two essential functions: it allows air IN to replace contents as they are drawn out, and it allows air displaced by incoming water, fuel or waste to get out. Therefore, it's absolutely essential that all tank vents be kept open, because unless air can be pulled in through the vent to replace the contents being pulled out, a vacuum is created in which nothing more can be removed--but in which strong suction can crack the tank (not likely in fresh water and fuel systems, but highly likely if a waste holding tank is connected to a strong pumpout). A pressurized tank can have equally disastrous consequences--anything from a geyser when the deck fill or deck pumpout cap is removed to a backup in the toilet, to blown out fittings, to a burst tank.
99% of all vent blockages occur at the through-hull. Dirt daubers build nests in the opening, insects fly or crawl in, get stuck and die, dust, dirt and pollen clog screens in the thru-hull...
On sailboats, however, heeling can send tank contents into the vent line, also creating a blockage at the tank in both that end of the vent line and the vent fitting on the tank. Overfilling the tank can also cause this on any boat. This will require removing the vent line from tank (it would be a very good idea to open the deck pumpout fitting cap to relieve any pressure before disconnecting any hoses!
So start by using a screwdriver blade, icepick--whatever works-to clean out the vent thru-hull. If that doesn't clear the vent, you'll have to clean out the other end of the vent line too. Do not use the toilet again until the vent is clear.
I suggest you also check out the link in my signature here...it goes to a comprehensive "marine toilets and holding tanks 101" manual that will help you learn how to cure most "head aches" including blocked tank vents, but PREVENT 'em...and as you're already learning, prevention is a lot easier that cure!