Seppi won 7-6 3-6 5-3 after two hours 35 minutes when the third seed retired after injuring his leg following a tumble on the greasy surface after calling for the match to be halted an hour earlier because of bad light.
Officials halted play for around 20 minutes with Seppi leading 4-0 in the final set before the match resumed in an almost deserted stadium.
Tipsarevic fought back to 4-3 before play was halted for another 10 minutes when he was strapped up after being wrong-footed by a return at the baseline, splaying his legs as he fell to the ground.
With Wimbledon starting on Monday and the tournament already hit by rain which washed out play on Friday, officials were keen to get the match finished.
Tipsarevic, though, was unhappy with the conditions. He asked for play to be halted at the start of the third set but was overruled by the tournament supervisor.
Complaining soon after because he said "the scoreboard was shining," some spectators, wrapped up in hats and scarves in the chilly conditions, shouted back at him "get on with it."
As conditions worsened Tipsarevic complained more loudly and with Seppi leading 5-3, 15-0 in the final set, he decided enough was enough.
Both men were playing their second match of the day after Tipsarevic beat Japan's Kei Nishikori 6-2 6-4 in his semi-final earlier and Seppi eliminated Russian Igor Kunitsyn 6-4 2-6 6-4.
World number 30 Tipsarevic had previously reached three ATP finals and lost them all, with the most recent defeat coming in the Delray Beach tournament in the United States in February when he lost to Juan Martin del Potro of Argentina.
Seppi was taking part in his first ATP final for four years.
(Created by Mike Collett; Editing by Tony Jimenez)