I would assume that Egypt paid. They have by far the biggest incentive to clear the canal asap. They will presumably now enter a lengthy legal dispute to try and get their money back from the shipping company.
My understanding is that the Suez Canal Authority will have to pay, but also that the SCA requires the use of "pilot" captains that maneuver the boats through the canal, which means that the issue was squarely the fault of the SCA.
