Can my students sit Cambridge O Level Physics 5054 with Cambridge O Level Combined Science 5129?

No, not in the same series of exams. In a single series of exams some combination of syllabuses are not allowed and you should refer to section 5 ‘What else you need to know’ in the Physics 5054 syllabus to find out the exceptions when combining O Level Physics 5054 with other Cambridge International syllabuses.