The Swede appeared to strain a muscle in his side in innocuous fashion early on, and lasted barely 15 minutes before making way for Ezequiel Lavezzi.
However, in his absence, Lucas opened the scoring in the 26th minute and Edinson Cavani doubled their advantage just before the hour mark to score his first of the campaign and give PSG their first victory in Ligue 1 after last weekend's 2-2 draw at Reims.
"At first I thought he had taken a knock, but no, it was as he was turning that he hurt himself in the side. It is a strange injury," said PSG coach Laurent Blanc of Ibrahimovic.
"I am not a doctor. I don't know if it is serious, but knowing Ibra, for him not to finish the match the pain must have been quite intense. We will need to see with the medical staff if it is serious or not."
Meanwhile, a comfortable home victory was also marred by a reported incident in the tunnel at full-time, with images showing PSG's Thiago Motta with a bloodied nose after apparently being hit.
Bastia had never beaten PSG away from home in the top flight but they were optimistic of springing a surprise thanks to the influence of their new coach Claude Makelele, the former Paris captain who gave up his role as assistant coach at the Parc des Princes to take over in Corsica this summer.
Makelele's men had recovered from 3-1 down to draw 3-3 at home to Marseille last weekend, but they rarely looked like doing anything similar on occasion as PSG's expensive summer signing David Luiz was afforded a gentle stroll in the late afternoon sunshine for his Ligue 1 debut.
"He didn't have much to do, but we didn't buy him so that he does a lot. We signed him because he is a good defender," said Blanc of the Brazilian, signed from Chelsea in June for a reported €50 million ($67.1m), a world record fee for a defender.
The 27-year-old might not have started this match had his compatriot and captain Thiago Silva not been ruled out for several weeks with a hamstring injury suffered in friendly win against Napoli, and Blanc could have done without losing his stand-in skipper Ibrahimovic as a result.
Blanc also took Gregory van der Wiel off at half-time, the Dutch right-back taking a knock from Brandao's knee and making way for Serge Aurier, who made his home debut after signing on loan from Toulouse.
Before that, Van der Wiel had been the creator of the game's opening goal, his cross from the right being met first-time on the volley by the unmarked Lucas at the back post.
The reigning champions then struck again in the 57th minute when Uruguay star Cavani brilliantly controlled a quickly-taken Marco Verratti free-kick inside the area before volleying past Bastia's on-loan PSG goalkeeper Alphonse Areola and into the net.
"My team never played," said Makelele, who added that he will take action if one of his players is found guilty of a post-match assault on Motta.
"If my player started it, it is not worthy of a professional player and there will be punishment."
, Lille warmed up for the first leg of their Champions League play-off against Portuguese giants FC Porto by beating promoted Caen 1-0 courtesy of a second-half penalty from Belgian international forward Divock Origi.