The scores were locked at 10-10 and Italy looked on course to secure a second successive draw when Paterson accepted a chance from long range with three minutes remaining.
Paterson had scored his side's only try in the first half but Italy, who now finish with the wooden spoon, proved difficult opponents to shake off.
Scotland only just edged an entertaining, albeit error-filled, first half 10-7 after Italy made much the better start.
The Azzurri, playing in their change strip of white, went straight onto the attack and were rewarded with the opening try after just five minutes.
Ramiro Pez had already troubled the Scots with one kick and they had no answer as he delicately chipped over the defensive line for Mirco Bergamasco to collect and dive over.
Pez added the extra two and Scotland suffered a further blow when returning half-back Chris Cusiter was forced off just 10 minutes into his comeback with a shoulder injury.
The visitors responded to the setbacks well and soon recovered as they powered forward and the dependable Paterson crashed over for a self-converted try.
Paterson could have had a second soon after following another good break but Italy again threatened when Bergamasco chased his own kick and ran close to the line. Pez also missed with a drop goal attempt.
Scotland nudged themselves ahead in the final minute of the first half when Gordon Ross landed a straightforward drop goal from in front of the posts.
Italy squandered a great chance to reclaim the lead early in the second half when Pablo Canavosio pounced on a loose ball after some poor work by Rory Lamont and Mike Blair but Pez knocked on close to the line.
Pez made no mistake, however, after 58 minutes as he levelled the scores with a long-range penalty.
Neither side were willing to give much as the clock ran down but Paterson made no mistake when offered his late chance to secure Scotland's first away win in the competition for four years.