The Montreal-based company completed the $2.64bn (£1.65bn) acquisition of its larger Anglo-Dutch rival Logica in August and recorded a related charge of C$248m in the quarter.
CGI posted a loss of C$168m, or 58 Canadian cents per share, compared with a profit of C$70m, or 26 Canadian cents per share, a year earlier.
Analysts on average expected earnings of 41 Canadian cents on revenue of C$1.65bn.
Revenue rose 60 per cent to C$1.61bn.
The company, which provides technology outsourcing and consulting services, booked C$1.52bn in new contracts, extensions and renewals, up three per cent from a year earlier.
“The integration of Logica into the CGI operational model is well underway and being implemented as planned,” said president and chief executive Michael Roach.
“We continue to expect the combination to generate an accretion rate of 25 per cent to 30 per cent in fiscal 2013, excluding acquisition related and integration costs.
“We are well positioned operationally and financially to continue to execute our profitable growth strategy in F2013 and beyond,” he added.