The two coaches were bitter rivals during their respective spells in charge of Barcelona and Real Madrid in La Liga and renewed their rivalry on Friday night.
And Pique took to Twitter to express his delight moments after Javi Martinez's strike for Bayern made it 2-2 in extra time and took the game to a penalty shootout.
He tweeted: ""Football is the best!! Orgasmic!!".
After the game the Barca defender added: "Congratulations to Bayern München and Pep Guardiola for winning the European Super Cup!"
Fernando Torres opened the scoring for Chelsea on the night before Franck Ribery made it 1-1 and ensured the two sides battled it out for another 30 minutes of extra time.
Eden Hazard's strike looked to have given Chelsea the win but a last-gasp goal from Martinez meant penalties ensued, with Bayern prevailing 5-4 after Romelu Lukaku's miss from 12 yards.
David Alaba, Toni Kroos, Philipp Lahm, Ribery and Xherdan Shaqiri all held their nerve to give Guardiola a win over his old adversary.