If I understand your scenario, you now have a bench warrant issued for your arrest, for a civil infraction, that went unresolved pending the outcome of your criminal case. Assuming this is true, as far as the civil infraction is concerned, all you will have to do is go to the court where the warrant is issued and pay all fines, costs and late fees associated with the ticket. That will act to terminate the bench warrant.
There is of course another issue to consider, given that you are on probation. Your failure to pay a ticket and subsequent bench warrant may be viewed by a probation officer as a violation of law that could trigger a probation violation. Most POs will be understanding, but you should bring this to their attention immediately. The potential outcome could be worse should they learn about it through some other means.