Lobo could probably speedblitz him to death, but it would be an awesome fight. I recon Apocalypse could win if he used all the powers he had at his advantage though.
I can't really imagine Apocalypse trying to run away, so odds are Apoc would pour everything he has into Lobo, and Lobo would resist or heal from it and end it.
He's stronger and heals better, but that's about it.
Apocalypse has an arsenal of powers at his disposal, I'm not sure if Lobo can withstand that. Matter manip, time manip, reality warping, energy absorption, class 100+ strength, control over his own body, access to incredibly advanced technology, possible telepathy and telekinesis. He has also regenerated from a drop of blood, but that takes a lot of time.
Keep in mind that we haven't seen a lot of fights with Apocalypse at full power, most of his showings are with him being depowered.
Lobo lifted the entire weight of the universe once?
Vast Super strength
Near Invulnerability
Super Speed
Super human endurance
Fantastic Leaping Ability
Tracking ability allows him to trace prey across galaxies
Can survive unaided in the vacuum of space
Unparalleled brawler
Can replicate himself into an army of clones
Immortality
Can take possession of other living being
Can continue fighting in a spirit form
He can instantly analyze any opponent, weighing up their abilities and defenses perfectly, giving him exact knowledge of their Achilles Heel or weak spot
He doesn't have Super Speed, I've never seen him Speedblitz anyone. I suppose he was able to punch Superman fast that one time, but that's about it. If you want a list like that.
Energy absorption
Energy projection
Matter manipulation
Regeneration
Superhuman endurance
Near invulnerability
Superhuman strength
Can create/summon things to figth for him
Shapeshifting
Complete control over his body at a molecular level
Time manipulation
Reality warping (small time)
Telekinesis
Telepathy