Lois Diony had fired the visitors into the lead in the 10th minute but Sylvian Marveaux drew level for Lorient a few minutes after restart from the interval.
Waris then converted a 60th minute spot-kick which gave his side the lead.
Soon thereafter, Jordan Loties drew Dijon level but Les Merlus were awarded another spot kick in the 76th minute. The Ghanaian duly stepped up once again but this time fluffed his effort before seeing his side go down 3-2 in regulation time, Pierre Lees Melou with the sucker-punch. This was the second time Waris has missed the penalty in three matches, having also squandered one in Lorient's 3-1 win over Guingamp recently.
The defeat saw Lorient occupy the bottom spot of the Ligue 1 log with 18 points from 22 matches.
Despite his snub by Avram Grant from the Black Stars’ squad for the ongoing Africa Cup of Nations in Gabon, the 25-year-old has been in glittering form for his struggling side, netting three times in three outings so far in the New Year.
And with question marks hanging over Asamoah Gyan’s availability for the Afcon Quarter-Final clash against DR Congo on Saturday, perhaps Waris would’ve been a perfect replacement.