The Montreal-based company completed the $2.64 billion acquisition of its larger Anglo-Dutch rival Logica in August and recorded a related charge of C$248 million in the quarter.
CGI posted a loss of C$168 million ($169 million), or 58 Canadian cents per share, compared with a profit of C$70 million, or 26 Canadian cents per share, a year earlier.
Excluding items, the company earned C$100 million, or 37 Canadian cents per share.
Analysts on average expected earnings of 41 Canadian cents on revenue of C$1.65 billion, according to Thomson Reuters I/B/E/S.
Revenue rose 60 percent to C$1.61 billion.
The company, which provides technology outsourcing and consulting services, booked C$1.52 billion in new contracts, extensions and renewals, up 3 percent from a year earlier.
Shares of CGI, which has a market value of C$6.6 billion, closed at C$24.05 on the Toronto Stock Exchange on Tuesday. The company’s New York-listed shares closed at $24.22.
Reporting by Krithika Krishnamurthy in Bangalore; Editing by Sriraj Kalluvila