Promoted Freiburg also scored twice in the last five minutes to beat Borussia Moenchengladbach 3-1, Bundesliga debutants RB Leipzig stunned Borussia Dortmund with an 89th minute goal and Darmstadt snatched a last minute win over Eintracht Frankfurt.
Mario Gomez drew a blank on his debut for VfL Wolfsburg, who were held 0-0 at home by Cologne, while Hertha Berlin's 2-0 win at Ingolstadt left them and Bayern Munich as the only teams with six points from their first two games.
Pohjanpalo immediately transformed the game after coming on in the 72nd minute with his side trailing to U.S. forward Bobby Wood's goal just before the hour.
The Finland international, who has returned to Leverkusen after two years on loan at Fortuna Duesseldorf, headed in Julian Brandt’s cross in the 79th minute to equalise.
The 21-year-old then put Leverkusen ahead with a clinical finish in the 90th minute and struck again in stoppage time as they picked up their first points of the season.
Dortmund's hopes of challenging Bayern for the title suffered an early blow at Leipzig, who were only founded in 2009 and were playing their first-ever home Bundesliga match.
Guinea midfielder Naby Keita was Leipzig's hero, turning the ball into the net after Oliver Burke played the ball across goal from the byline.
Dortmund had wasted a chance just minutes earlier when Andre Schuerrle hit the crossbar instead of passing to an unmarked team mate.
Thorgan Hazard gave Gladbach a first-half lead with a delightful curling shot from 30 metres at Freiburg but Maximilian Philipp levelled with an equally superb strike in the 54th minute.
Philipp volleyed another with five minutes to go and Nils Petersen completed Freiburg's win by converting a penalty for the club's first three points since returning to the Bundesliga after a season in the second tier.
(Writing by Brian Homewood, editing by Alan Baldwin)
