Jones scored three times, as did Andrew McCutchen, who went 4-for-5 with an RBI for the Pirates.
Neil Walker chipped in with two hits, including a solo homer and a two-run double, while Casey McGehee supplied three hits with a pair of RBI, as Pittsburgh romped in the opener of a four-game series.
The second-place Pirates entered the contest one game behind Cincinnati in the National League Central.
James McDonald (8-3) won his third straight start, working around five walks and four hits to hold the Astros to two runs over seven innings.
Houston starter Jordan Lyles (2-5) was lit up for seven runs on nine hits over four frames.
Scott Moore socked a solo homer for the Astros, who dropped their fifth straight.