Charging 2 super capacitors in series
If you connect them in series you have to ensure the voltage is divided evenly at all times so it never goes over 2.7V for each one. Normally this is true just by regular series connection, but if one shorts out or something alike then you will end up applying 5V the other capacitor.







simulate this circuit &ndash; Schematic created using CircuitLab

edit: I added the schematic of the circuit, now the values of the R are not really well thought off, but if you can switch them out once the voltage of your capacitors is close to 2.2V then their value does not matter much as long as they are equal, it is better if they are large so it doesn't load your source

I don't know what is your final design, but if you can connect a large resistor in parallel to each capacitor, they would help to ensure the voltage stays somewhat even in  case anything happens. You only need them during charging so you could add a switch to each resistor to cut them out of the circuit so they dont discharge your capacitors after you turn off your voltage supply.