Zverev, seeking his third ATP Finals title, followed up his defeat of Rublev with a straight-set win against Norwegian sixth seed Ruud.
Ruud only missed six of his first serves in the first set but Zverev dominated the tie-break after the opening 12 games yielded no break points.
With an hour and 20 minutes gone, Zverev finally secured a break to go 5-3 up in the second set and served out to love for victory.
“I think it was a very good match actually from both of us,” he said. “I’m happy to win today but it was very, very close.”
On Thursday, American Taylor Fritz faces Australian Alex de Minuar (13:00 GMT) in the final round of Ilie Nastase Group matches.
World number one Jannik Sinner will reach the last four if he claims a set against Daniil Medvedev (19:30), and will top the group with a third straight win.