Nova connected with James on scoring passes of 69 and 31 yards and added tosses of 38 yards to Leonte Carroo and 19 to John Tsimis as the Scarlet Knights (2-0) scored 31-straight first-half points to overcome an early deficit.
James, who had three TDs in the season-opening win over Washington State, also scored on a 7-yard run for Rutgers, which will play its first Big Ten Conference game here next weekend against Penn State.
The last few minutes of the game were finished as lightning fell near High Point Solutions Stadium. Officials let the game continue despite some audible concern by the crowd after seeing the lightning.
The Scarlet Knights came into the game worried about looking past the Bison to the Nittany Lions, who are their closest Big Ten opponent. There might even be a rivalry brewing after Penn State coach James Franklin said Rutgers had no chance recruiting in New Jersey against the Happy Valley crowd.
Howard, which was shutout by Akron last week, added to Rutgers' concerns. It forced a 3-and-out on the opening series and then went 41 yards on its opening drive to take a 7-0 as Freeman scored untouched on a counter.
That woke up the Scarlet Knights, who are now 11-0 against Mid-Eastern Athletic Conference schools.
Nova, 15 of 19 for 282 yards, drove the Scarlet Knights to scores on their next four possessions. Kyle Federico cut the gap to 7-3 with a 42-yard field goal. After holding Howard without a first down, Nova caught the Bison on a blitz on the next series and hit a wide-open James on a swing pass for the 69-yard play down the Howard sideline.
Nova found Carroo on a slant on the Scarlet Knights' next possession and James capped a three-play, 31 yard drive with his run after Quentin Gause forced a fumble by Freeman.
James' second touchdown came after Turay Kemoko blocked a 28-yard field goal attempt by John Fleck late in the half. A 36-yard pass from Nova to Andre Turzilli preceded James' 31-yard TD catch, also on a swing pass.
Parker's run cut gap to 31-13, but Nova found Tsimis all alone at the 2-yard line for his fourth touchdown, one shy of career best set against Arkansas last season.
McGhee and Tusan closed out the scoring for Howard.