Ronaldo was presented with a special jersey before kick-off by Juventus president Andrea Agnelli to mark his 700th career goal scored playing for Portugal during the week.
The 34-year-old hit his 701st after 19 minutes in Turin, with Pjanic adding a second eight minutes after the break following a blunder by Brazilian defender Danilo, who had earlier pulled Bologna level.
The defending champions are now four points clear of second-placed Inter Milan, who travel to Sassuolo on Sunday.
Atalanta stay third after throwing away a three-goal lead to draw 3-3 with Lazio in Rome, with fourth-placed Napoli closing the gap to just one point after Arkadiusz Milik's double saw off Verona.
Bologna coach Sinisa Mihajlovic returned to the bench in Turin after his second course of chemotherapy as he battles cancer.
And the visitors were given reason to hope for a rare point against the Turin giants when Danilo responded to Ronaldo's opener with a 29th-minute volley.
But Pjanic sealed victory with his third goal in four games in the 54th minute amid chaos in front of the Bologna goal.
Bologna keeper Lukasz Skorupski denied Ronaldo and in-form Gonzalo Higuain late before both the crossbar and Gianluigi Buffon frustrated Federico Santander's push for a last-gasp equaliser for the visitors who slip to 12th place.
Immobile punishes Atalanta
Serie A leading scorer Ciro Immobile's late brace of penalties helped Lazio wipe out a three-goal deficit in a thrilling 3-3 draw with Atalanta.
Atalanta, who travel to Manchester City in the Champions League on Tuesday, had led 3-0 with 21 minutes to go at the Stadio Olimpico.
But Immobile scored from the spot on 69 minutes and less than 60 seconds later set up Joaquin Correa for the second, before capping the comeback two minutes into injury time with his ninth goal in eight league games this term.
"There was a loss of focus on our part, but it's hard to neutralise a team like Lazio at home," said Atalanta coach Gian Piero Gasperini, who was furious with both penalties awarded.
"With penalties, nobody can understand a thing nowadays.
"Immobile went for a walk, felt someone touch him slightly and dived. I've seen it again and it's obvious to me.
"Even more, on the second penalty, Immobile put his foot in front of De Roon. That's not a penalty either."
Star Atalanta striker Duvan Zapata was sidelined with an injury suffered on international duty with fellow Colombian Luis Muriel taking his place.
The forward bagged a first-half double as Lazio struggled initially in a rematch of last season's Italian Cup final which the Romans won.
Muriel put the visitors ahead on 23 minutes when Robin Gosens played the Colombian in on goal.
He scored his second five minutes later from a free-kick, with Alejandro Gomez netting the third eight minutes before the break.
But the visitors lost momentum after the hour mark.
Immobile got one back from the spot after being brought down by Jose Luis Palomino and then combined with Correa for their second.
Immobile earned a late penalty after a Marten de Roon foul, celebrating wildly after converting to grab a dramatic point before Lazio's Europa League trip to Celtic next week.
"I'm losing years of my life kicking penalties in the 90th minute," said 29-year-old Immobile, after scoring his third league goal from the spot this season.
Polish striker Milik scored in either half as Napoli got back to winning ways at the Stadio San Paolo with a 2-0 victory, after a goalless draw at Torino before the international break, to stay fourth, one point behind Atalanta, before their Champions League trip to Salzburg.
"I started the season with fitness problems so I'm hungry now for goals," said Milik, who also scored as Poland qualified for Euro 2020 during the week.
Verona drop to 13th place.