The centre-back played the full 90 minutes, while Bolton team-mate Dion Charles came off the bench for the final half hour.
Adam Cerin got the decisive goal inside the opening five minutes with a fine free kick. The hosts were reduced to 10 men when Southampton youngster Shea Charles was shown a second yellow card just before the hour mark.
The result leaves Michael O’Neill’s side fifth in Group H on six points, with both of their victories coming against San Marino. Their remaining qualifiers are against Finland and Denmark next month.
Slovenia are currently top of the group, above Denmark on goal difference after the Danes beat San Marino 2-1.
Third-place Kazakhstan still have a chance of qualifying but need to gain four points on the top two in the final games. There would also need to be a drastic swing in terms of goal difference.
Toal’s first call-up to the senior squad came in March after breaking into the Bolton side following his move from Derry City.
Prior to the international break, Ian Evatt told The Bolton News: “He is a brilliant young player with a huge future for that country, and they have had some wonderful centre-halves.
“I know Craig Cathcart very well and he was one of the best centre-backs I played with in my career. Craig is coming to the end of his career now and I think Northern Ireland have some young players who deserve an opportunity, and Eoin is one of those in my opinion.
“The squad is going through a transitional phase at the moment, but I have no doubt at all that Eoin can go and be a part of it for a very long time.”
Toal will be hoping to build on his international debut when Wanderers host Northampton in League One this weekend.
The 24-year-old will be keen to get a consistent run of games under his belt, having missed the start of the campaign through injury. He also served a one-match ban following his sending off at Reading.