Pennington, 19-years-old and a feature of England under 19s run to the semi-finals of the World Cup in New Zealand in the winter, claimed four for 53 from 16 hostile overs in only his third Championship appearance.
He saw Kane Williamson dropped at first slip on 18 before lunch, with the New Zealand captain going on to make 87 off 131 balls - the standout innings of a shortened day played out in testing conditions.
Worcestershire reached close at 39 without loss from 13.4 overs of their reply, with 20.2 lost to bad light and then rain from 5pm onwards.
Jack Brooks also made 38 down the order as Yorkshire recovered from losing four mid-afternoon wickets in 16 balls, slipping to 155 for eight.
Brooks hit two big sixes, including a pull off Pennington, as he dominated a 56-run stand for the ninth wicket with Matthew Fisher (20 not out).
Earlier, New Zealand captain Williamson shared 88 for the fifth wicket with Jonny Tattersall (27) as they recovered from 63 for four either side of lunch.
They were two of those aforementioned four quick wickets to fall for four runs as the White Rose fell from 151 for four in the 49th over to 155 for eight in the 52nd.
Tattersall was brilliantly caught one-handed high above his head by Daryl Mitchell at second slip off Pennington before Williamson chopped on trying to cut Moeen Ali’s off-spinners.
Before lunch, Pennington had Gary Ballance and Tom Kohler-Cadmore caught at point within three balls in the 23rd over (63 for four), with the latter looping a lifter to point off a combination of glove and shoulder.
Pennington used pace and carry, nip off the pitch and uneven bounce to his advantage, while another seamer Ed Barnard got the ball swinging and finished with three wickets. Captain Moeen added two.
Williamson was calm and composed, but he was troubled.
After the drop, he was hit on the right hand by a short ball from South Africa left-arm quick Wayne Parnell, although he later hit him for four successive boundaries - three of them driven.
Worcestershire started their reply with 34 overs remaining in the day and the signs were encouraging as they search for a second win in nine matches this season.
Openers Mitchell and Tom Fell, opening for the first time in Championship cricket, were able to take the gloss off the new ball by reaching 16 and 21 not out respectively before umpires Tim Robinson and Neil Mallender called a halt to play with the light closing in.
It is a long way from panic stations for Yorkshire, but they could do with striking early in the morning to ease some of the tension amongst the home faithful.