Boca, with 29 points from 15 matches in the Clausura standings, are a point ahead of Tigre and Newell's Old Boys after their match on Friday ended in a 3-0 win for Tigre thanks to Carlos Luna's hat-trick.
Viatri came on in the second half at Racing's Cilindro for his first appearance in seven months following the injury to his left knee and broke the deadlock in the 70th minute when he took a pass with his back to goal, turned and fired home.
With eight minutes to go, fellow striker Nicolas Blandi hit Boca's second when he scored from Pablo Mouche's pull back.
"It was a goal that helps me a lot spiritually, brings me lots of memories, the hard times I went through," an emotional Viatri told reporters.
"The one up there [God] shone a bit on me."
Promoted Belgrano, the team that consigned Boca's arch-rivals River Plate to the Primera B Nacional (second division) by beating them in a promotion-relegation play-off last June, secured their place in the top flight for another season with four matches to spare after a surprise 1-0 win at Velez Sarsfield.
Belgrano are mid-table but they now have enough points in the 2011/12 season comprising the Apertura and Clausura to ensure their average is high enough to keep them out of relegation danger even if they lose their remaining four matches.
On Saturday, San Lorenzo lost 1-0 at Union worsening their relegation prospects with the possibility of having to face a play-off against River, joint second in the B Nacional. It would be the first such clash between two of Argentina's 'Big Five.'
"It would cause heart attacks," River coach Matias Almeyda was quoted as saying in the sports daily Ole.
Estudiantes won their second successive match since captain Juan Sebastian Veron returned from injury, beating bottom team Banfield 3-0.
