A consummate bowling performance by the Lions had seen the Cobras dismissed for just 255 after the visitors won the toss and chose to field, but Paterson and Hendricks made short work of the Lions top order before the visitors went to stumps on 36 for three.
While Hendricks had Stephen Cook caught behind, Paterson (2 for 8) dismissed Quinton de Kock and Dominic Hendricks to leave the Lions on 13 for three in the eighth over.
Neil McKenzie (15 not out) and Temba Bavuma (16 not out) steadied the reply, but the Lions remain 219 runs adrift.
The Cobras innings was reliant on a 139-run stand between Justin Ontong (88) and Yaseen Vallie (70) after Lonwabo Tsotsobe had struck twice early on.
Tsotsobe dismissed Omphile Ramela with the second ball of the day and also trapped Andrew Puttick lbw, while Hardus Viljoen got the better of Stiaan van Zyl as the Cobras slumped to 17 for three.
Ontong and Vallie dug them out of a hole, but both ultimately fell to Imran Tahir, who went on to dismiss Dane Vilas (34) and Shaheen Khan on the way to figures of 4 for 62.
Pumelela Matshikwe wrapped up the tail to match the two wickets claimed by Tsotsobe and Viljoen, but the Lions batsmen were unable to set the steady platform that could have given them the upper hand.