Short answer. Yes. Death totally extinguishes criminal liability, so the prosecution cannot continue against a dead accused and the case is dismissed as to him. Money penalties are treated separately: they are wiped out only if the death happened before the judgment became final, otherwise they survive against his estate.
What the law says
By the death of the convict, as to the personal penalties; and as to pecuniary penalties, liability therefor is extinguished only when the death of the offender occurs before final judgment.
Revised Penal Code, Article 89 — How Criminal Liability Is Extinguished. Read the full provision →
Death ends the case against the accused
Article 89 of the Revised Penal Code lists the ways criminal liability is totally extinguished, and the first of them is the death of the convict, as to the personal penalties. Personal penalties are those that can only be served by the person himself — imprisonment and the restrictions that go with it. Nobody else can serve them, and punishment cannot be inherited. So where an accused dies while the case is pending, the criminal action against him is at an end and the court dismisses it as to him. Co-accused are unaffected; the case continues against everyone still living.
Money penalties turn on the timing
The article draws a sharp line for pecuniary penalties — fines and the costs the court imposes. These are extinguished only when the death of the offender occurs before final judgment. The reference point is finality, not the day sentence was pronounced: a judgment on appeal or still within the period to appeal is not yet final. Die before that moment and the monetary penalty dies too. Die after the judgment has become final and the obligation has already attached to the offender's patrimony, so it is enforced against what he left behind rather than forgiven.
What the victim may still be able to pursue
Extinguishing the crime also extinguishes the civil liability that arises purely from the crime, because there is no longer an offence on which to base it. That is not the end of every claim. Where the same facts give rise to an obligation from another source — a contract, a quasi-delict, or a duty imposed by law itself — that claim stands independently and may be brought as a civil action against the estate or the persons answerable, subject to the rules on filing claims in estate proceedings and to the applicable time limits. The measure of what can be recovered may differ from what the criminal court would have awarded.
The other ways liability ends, and one modern caveat
Death is one item in a longer list. Criminal liability is also totally extinguished by service of the sentence, by amnesty, which completely extinguishes the penalty and all its effects, by absolute pardon, and by prescription of either the crime or the penalty. Read the whole Code with one correction in mind: where its provisions still speak of the penalty of death, Republic Act No. 9346, enacted in 2006, prohibits the imposition of the death penalty in the Philippines, and the courts impose the Code's next gravest penalty in its place. The older text remains on the page, but that prohibition governs.