Short answer. Likely yes. The Labor Code counts as hours worked all time an employee is suffered or permitted to work — if your supervisor knew you kept working and did not stop you, that time falls within this definition, separate from time you were simply required to be on duty.
What the law says
Hours worked shall include (a) all time during which an employee is required to be on duty or to be at a prescribed workplace; and (b) all time during which an employee is suffered or permitted to work.
Labor Code, Article 84 — What Counts As Hours Worked. Read the full provision →
Two separate categories count as hours worked
Article 84 defines hours worked with two distinct categories, not one. The first is all time during which an employee is required to be on duty or to be at a prescribed workplace — time governed by an instruction or schedule. The second, separate category is all time during which an employee is suffered or permitted to work. Your situation fits squarely within that second category, which does not depend on whether you were formally required to keep working at all.
Why 'suffered or permitted' matters for your situation
"Suffered or permitted to work" captures exactly the scenario in the question: work the employer did not formally schedule or order, but knowingly allowed to happen. If your supervisor was aware you were continuing to work past your shift and did not stop you, that is functionally permitting the work to continue — the employer's knowledge and inaction is what brings the extra time within this category, rather than requiring a formal instruction to keep working.
Why this distinction protects employees
If hours worked were limited only to time an employee was formally required to be on duty, an employer could benefit from extra work simply by never explicitly ordering it, while still knowingly allowing it to happen. Article 84's second category closes that gap: work the employer suffers or permits, even without an explicit directive, still counts. This puts the focus on whether the employer knew and allowed the extra work to occur, not on whether a supervisor formally told you to keep going.
What this does not automatically cover
This category depends on the employer's knowledge or ability to know, not simply on the fact that work happened. Time spent working entirely without the employer's awareness, in a way the employer had no reasonable opportunity to notice or stop, sits on much weaker footing than the situation in the question, where the supervisor was specifically aware you were still working and chose not to intervene at all.