Thomas led the way with 22 points, eight rebounds, five assists and three steals on 9-of-22 from the field in the victory, while three-star Pittsburgh commit
Brandin Cummings contributed a team-high 25 points on 7-of-15 from the field and 9-of-10 from the free throw line.
Neumann-Goretti (26-4) had multiple good looks at potential game-tying baskets in the final seconds before Cummings secured the game-clinching rebounds and knocked down a pair of free throws with 0.5 seconds remaining.
The closely contested championship game saw 13 lead changes and 11 ties, while both teams saw their biggest lead grow to seven points.
Neumann-Goretti went ahead 15-14 at the end of the first quarter before the game was tied 28-28 at the half. Lincoln Park Performing Arts (31-1) surged ahead 44-41 at the end of the third quarter before pulling out the four-point victory.
The loss marks the first state title game defeat for Neumann-Goretti — which was 9-0 in previous championship games.
Four-star Baylor commit
Robert Wright III finished with a game-high 27 points on 10-of-20 shooting in the loss for the Saints.