The Dons, who had not won in the league at Parkhead since 2004, looked on course for a point after Commons' 35th-minute effort was cancelled out by former Hoops forward Niall McGinn in first-half stoppage time.
It stayed that way until the death, with Georgios Samaras and McGinn both hitting the woodwork as the sides swapped chances in the second half.
Boerrigter, on for Teemu Pukki, then prodded the ball over the line in the first minute of added time after Jamie Langfield had parried a Virgil van Dijk header.
The Dons were stunned again moments later when Commons slammed the ball in from close range to extend the leaders' unbeaten league run to 13 games.
Inverness kept the deficit on Neil Lennon's men to five points after edging to a 1-0 victory over St. Johnstone.
A close-range effort from the prolific Billy McKay decided the contest after a matter of minutes as both teams cancelled each other out in the remainder of the game.
The score was McKay's tenth league goal of the season and ensured he would remain at the top of the Premiership's goalscoring charts.
Motherwell remain within touching distance in third place after a 2-0 win at lowly Kilmarnock.
Strikers John Sutton and Henri Anier were on target to take their tally to 11 league goals between them after netting in the 55th and 88th minutes respectively.
The result leaves Kilmarnock in the relegation play-off places and above only Hearts, who needed a last-gasp strike from Ryan Stevenson to earn a 2-2 draw at home to ten-man Ross County.
Melvin De Leeuw put the visitors ahead for a second time in the opening stages of the second half after Graham Carey's 23rd-minute strike was cancelled out almost straight away by Callum Paterson.
The Staggies were reduced to ten men when captain Richard Brittain was shown a second yellow card and Stevenson levelled with two minutes left.
Jackie McNamara's men were comfortable winners in the end, with further goals coming from Andrew Robertson and Brian Graham, with Aaron Muirhead having levelled for Partick, whose cause was not helped by red cards for Conrad Balatoni and Stuart Bannigan.
The new Easter Road boss may not have had a win to celebrate at the end of the goalless Scottish Premiership encounter at St. Mirren Park, but he would have taken some satisfaction from ending a run of four straight defeats endured by the Edinburgh side before he took over the hotseat in Leith.