The Italy great had set up two goals, one for Stephan El Shaarawy and the other for Alessandro Florenzi, as Roma took a 3-1 lead at the Stadio Olimpico on Friday (AEDT).
But the Serie A side had to settle for a point in the Europa League after late goals from Dominik Prokop and Olarenwaju Kayode for the visitor.
The result keeps Roma top of Group E, but it is level on points with Austria Vienna and just two clear of Astra, who won 2-1 at Viktoria Plzen.
Raphael Holzhauser put Vienna ahead with a fine volley into the bottom corner before Roma took control.
El Shaarawy struck twice before half-time, the latter following a Totti pass, before the veteran's brilliant cross allowed Florenzi to volley in at the back post.
But Prokop pulled a goal back before a dramatic 84th-minute equaliser by Kayode for Vienna ruined Totti's milestone appearance.