Como dizer "Pagar a diferença" em inglês

to pay the difference
[expression]
>> pagar a diferença.

Examples:

1) They were very apolegetic, but we needed to pay the difference after all.
>> Eles sentiram muito, mas precisamos pagar a diferença no fim das contas.

2) You will need to pay the difference in fare in addition to any charges.
>> Você(s) precisará(ão) pagar a diferença na tarifa, além de quaisquer encargos.

3) Can I pay the difference later?
>> Eu posso pagar a diferença mais tarde?

Note: The third sentence sounds very formal. You can make use of the sentence Can I pay next time?, which means you cannot pay something now and you intend to pay later.
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to make up something
[phrasal verb]

Related term: to make up (for) the difference = to provide the difference.
>> compensar a diferença
>> valer [a diferença] (informal)
>> pagar o que faltou / o resto / o restante .

Examples:

1) We’re US$3 short, but I will make up the difference.
>> Estamos sem três dólares, mas (eu) vou compensar a diferença.
>> Estamos sem três dólares, mas (eu) vou pagar mais tarde.

2) The plumber said he would refund us 15% of the charges to make up for the service being delivered so late.
>> O encanador disse que nos reembolsaria 15% das cobranças para compensar o serviço que estava sendo prestado tão tarde.

3) Mark is not a great dealer, but his politeness and patience really make up for the price of this car.
>> Mark não é um bom negociante, mas sua paciência e educação realmente valeram / compensaram o preço deste carro.

Note: The phrasal verb to make up for something means to take the place of something lost or damaged or to compensate for something bad with something good. In the context of providing something, we just use the phrasal verb without the preposition for, which means we are going to provide an amount that reaches a total. If we use the preposition in this case, we will emphazise how much something is valuable and needed to be paid or afforded immediately.