Adopting an unfamiliar 3-4-3 system, Bayern lacked a clinical edge against Jens Keller's side, despite enjoying a dominant start.
The champions secured a 10th-minute lead courtesy of Robert Lewandowski's first competitive goal for his new club, before the hosts responded just after the hour when debutant Xabi Alonso's clearance inside the six-yard box cannoned back off Benedikt Howedes and into the net.
Replays suggested that the ball may have come off the arm of the German left-back, but Guardiola was more concerned with how his side had failed to build on their impressive start at the Veltins Arena.
He said: "The first 25 or 30 minutes were our best in the last six months. After that we no longer controlled possession, so we no longer had a grip on the game. But we ran hard so it was good training and a good test for our legs."
The result will be seen as an early chance missed for Bayern, who head into the international break two points behind early Bundesliga pacesetters Bayer Leverkusen.
The Bavarians resume their campaign at home to struggling Stuttgart on September 13 and Guardiola hopes the prolonged break will help ease an injury list containing Rafinha, Franck Ribery, Javi Martinez, Bastian Schweinsteiger and Thiago Alcantara.
"We have two weeks without a game now and I hope most of our injured players can resume training," he added.
One bright note was the debut of Alonso, who signed from Real Madrid earlier this week and played in a central defensive role in Gelsenkirchen.
Despite his contribution to the Schalke equaliser, the Spaniard impressed his new manager.
"He will help the team a lot because he has a great quality," Guardiola said.
