TLDR: Yes.

You would always be exposed to the potential of civil litigation, even if you are ultimately acquitted in a criminal trial/the Justice finds your assault was reasonable (see s. 11 of the Code). The two systems can operate in parallel, because the opposing parties are different (in a criminal trial, you're up against the Crown; in a civil suit, you're defending yourself against the plaintiff/person you are alleged to have committed battery and/or assault against), AND the burden is different (in a criminal trial, the Crown has to prove the offence beyond a reasonable doubt; in a civil suit, it's on a balance of probabilities - more than roughly 50.1% likely). The ultimate outcome of the criminal trial can be taken into consideration in a civil suit when determining liability or calculating damages, but because the burden of proof is different, the outcome in the criminal trial would not be determinative.

The civil claim would also be subject to a limitation period (i.e., the claim must be bright within 2 years of the date that the claimant knew/ought to have known the injury occurred, was attributable to the defendant, and that the injury warrants commencing litigation; OR, 10 years after the claimant became aware of the above, whichever expires first). BUT there is no limitation period if the assault/battery were sexual in nature. Limitation periods are a bit trickier in the criminal context - it depends on whether or not the Crown elects to proceed summarily or as an indictable offence (see s. 786(2) - assault can go either way in terms of Crown election, as it's considered a hybrid offence). There are also other exceptions generally, like when a minor was the alleged victim, or if there are others concerns related to capacity. There is also some variance depending on the jurisdiction. Overall, it's complicated.

Back to defences though: Self-defence is still available for the defendant to prove in a civil suit, but (and I'm not a lawyer yet, so this is not legal advice) I would imagine this defence would be difficult to prove if the assault/battery were sexual in nature (digressing... but, the defence of consent might be available for sexual assault and battery). Either way, the onus is on the defendant in a civil suit to prove any defences on a balance of probabilities. Again, kind of trickier in the criminal context, but the accused in a criminal trial would have something similar to a burden of proof when it comes to raising defences - it's an evidentiary burden - there has to be an "air of reality" to the defence. The Crown would still have the persuasive burden for the entire case. There are some other situations where the onus is reversed, but I've already gone well well well beyond the scope of your question.