The modest club from the suburb of Sarandi, founded in 1957 by present Argentine Football Association president Julio Grondona and his brother, finished the 19-match championship with 38 points, two more than their closest challengers Tigre, who were held 2-2 at home by Independiente.
"This is a huge happiness, something fabulous," Arsenal club president, Grondona's son Julito, said.
"The smallest (first division) club in Argentina were champions, the one with the fewest followers."
Title holders Boca Juniors, winners of the Apertura in the first half of the season, finished five points adrift along with All Boys, who beat them 3-1.
Central defender Lisandro Lopez, no relative of his Argentine namesake who plays as a striker for Olympique Lyon, scored the winning goal midway through the first half.
Belgrano had two players sent off, defenders Luciano Lollo in the 56th minute and Claudio Perez in added time.
Tigre, who began the day equal on points with Arsenal at the top, went ahead in the 20th minute with striker Carlos Luna's 12th goal confirming him as the tournament's top scorer.
However, a brace from playmaker Patricio Rodriguez early in the second half put Independiente ahead before a late equaliser by Diego Morales with a penalty after the visitors' Osmar Ferreyra had been sent off.
Tigre's point was enough to save them from a playoff with a team from the Primera B Nacional (second division) for their top flight survival. While vying for the championship, Tigre were dangerously low in the relegation standings, a separate table based on team's average points over the last three seasons.
Boca, who had effectively kissed the title goodbye in an upset 3-0 home defeat by Arsenal last weekend, fielded reserves at All Boys as the first team were rested for the first leg of South America's Libertadores Cup final at home to Corinthians of Brazil on Wednesday.
Winger Emanuel Perea scored a hat-trick for All Boys before defender Gaston Sauro pulled one back for Boca one minute from time.
Banfield, who won the Apertura title two and a half years ago, were relegated after a 3-0 home defeat by Colon. The match was abandoned seven minutes from time when angry Banfield fans threw objects on to the pitch.
Colon's 39-year-old striker Esteban Fuertes marked the last match of his career with two goals for a championship tally of seven.
San Lorenzo's 3-1 home win over San Martin with two goals from their Uruguayan striker Carlos Bueno put them into a promotion-relegation playoff with Instituto, who finished third in the Primera B Nacional.
Although San Lorenzo finished in 12th place in the Clausura standings, they finished in the bottom four of the relegation standings.
San Martin, who had midfielder Mauro Bogado sent off after half an hour, also go into a playoff with former first division champions Rosario Central, the fourth-placed team in the B Nacional.
River Plate and Quilmes were promoted on Saturday as B Nacional champions and runners-up.