OK, so there are a couple of misconceptions here. First, as Codosaur has already pointed out, Cronus and Chronos aren't necessarily the same being -- they just have similar names.
On the other hand, Cronus and Chronos were confused with each other even in antiquity. In fact the Roman god Saturn, who the Romans associated with the Greek god Cronus, was sometimes regarded as a god of Time.
This gives us a reson to address the more fundamental misconception -- even if we're allowed to conflate the Titan Cronus with the personnification of Time, this doesn't grant him some sort of "superpower" to turn back time.
Tempus edax rerum, tuque, invidiosa vetustas, omnia destruitis vitiataque dentibus aevi paulatim lenta consumitis omnia morte!
(O Time, devourer of all things, and envious Age, together you destroy all that exists and, slowly gnawing, bring on lingering death.)
(Ovid, Metamorphoses, 15, Tr. Brookes Moore, availableat the Theoi Project)
The ancient Greeks and Romans didn't think of time as something that could be reversed -- this is in line with the fatalism that expresses itself time after time in their mythology. You couldn't cheat fate by going back in time and changing things.
Instead, Time was regarded as a force that devours everything and wears it away to nothing. This may have been something Goya had in mind when he painted his famous painting of Saturn:
(Source: Wikimedia Commons)
Finally, we can answer why Zeus won. The most facile reason is that he was fated to do so, because Fate already ruled the gods. More to the point, Zeus had some powerful allies. His mother Rhea, whose strategies had kept Zeus from being swallowed alog with his brothers and sisters. He had his brothers and sisters, whom Cronus had vomited up after Zeus gave him the drink Rhea concocted for the purpose. The Cyclopes and a couple of titans such as Prometheus allied with Zeus. Most important were the Hekatonchires or "Hundred-handed ones" imprisoned by Cronus's father Ouranos:
But when first their father was vexed in his heart with Briareus and Cottus and Gyes, he bound them in cruel bonds, because he was jealous of their exceeding manhood and comeliness and great size: and he made them live beneath the wide-pathed earth, where they were afflicted, being set to dwell under the ground, at the end of the earth, at its great borders, in bitter anguish for a long time and with great grief at heart. But the son of Cronos and the other deathless gods whom rich-haired Rhea bare from union with Cronos, brought them up again to the light at Earth's advising.
And blameless Cottus answered him again: `Divine one, you speak that which we know well: nay, even of ourselves we know that your wisdom and understanding is exceeding, and that you became a defender of the deathless ones from chill doom. And through your devising we are come back again from the murky gloom and from our merciless bonds, enjoying what we looked not for, O lord, son of Cronos. And so now with fixed purpose and deliberate counsel we will aid your power in dreadful strife and will fight against the Titans in hard battle.'
And amongst the foremost Cottus and Briareos and Gyes insatiate for war raised fierce fighting: three hundred rocks, one upon another, they launched from their strong hands and overshadowed the Titans with their missiles, and buried them beneath the wide-pathed earth, and bound them in bitter chains when they had conquered them by their strength for all their great spirit, as far beneath the earth to Tartarus.
(The Theogony of Hesiod. tr. Hugh G. Evelyn-White, lines 617 ff.), at http://www.sacred-texts.com/cla/hesiod/theogony.htm