Chopra had two spells with the Bluebirds, scoring 58 goals in 142 appearances, before he moved from South Wales to Suffolk for £1.5million over the summer.
His 51st-minute header put the Tractor Boys in front after Jason Scotland had cancelled out Rudy Gestede's opener.
However, Whittingham gave Cardiff the last laugh when he slotted home after Aaron Cresswell had handled in the area as the hosts ended a five-match losing run against Paul Jewell's side.
Ipswich extended their unbeaten run to five matches but it will come as scant consolation after they dominated for large periods.
Cardiff had several opportunities to snatch a win at the death but Ipswich goalkeeper David Stockdale denied Gestede and Don Cowie to ensure the spoils were shared.
Malky Mackay made five changes to the line-up that was defeated by Hull two weeks ago, with the most notable replacements coming up front where Gestede made his first league start to partner Robert Earnshaw.
In-form Ipswich came into the match looking for their third consecutive win after victories over the Seagulls and West Ham before the international break and they were unsurprisingly unchanged.
Despite making a bright start, the visitors failed to make sufficient inroads on goal, although Scotland's shot from the edge of the area did force Cardiff goalkeeper David Marshall into action early on.
Yet, in their first meaningful attack at goal, the hosts took a 19th-minute lead, with Gestede marking his maiden start with his first league goal.
Aron Gunnarsson rifled his throw-in from the left into the six-yard area, where Gestede was able to head home.
Despite taking the lead, the Bluebirds failed to capitalise and the game settled into a bit of a lull.
From out of nowhere, though, former Swansea striker Scotland levelled proceedings on the half-hour mark with a 20-yard blast that sailed into the bottom corner.
The equaliser helped the Tractor Boys settle to their task and Chopra nearly put the visitors in front shortly before the interval but his effort was narrowly wide.
Grant Leadbitter's strike from 12 yards forced Marshall to tip over the bar as Ipswich retained the initiative in the second half.
And it should have come as no surprise when Chopra gave Ipswich a well-deserved lead in the 51st minute.
Carlos Edwards' cross from the right channel was headed high into the net by Chopra - much to the chagrin of Cardiff's fans.
Cardiff pushed for an equaliser but they were almost caught on the break as Scotland forced Marshall to make another fine stop.
The Bluebirds were then given a lifeline when Cresswell appeared to handle the ball in the area and after referee Dean Whitestone deliberated with his linesman, a penalty was awarded.
Peter Whittingham made no mistake by placing his spot-kick into the bottom left corner in the 72nd minute.
With the bit between their teeth, Cardiff laid siege to the Ipswich goal and David Stockdale had to be at his best to deny Gestede from notching his second of the afternoon before Cowie also saw a header pushed wide by the Tractor Boys shot-stopper.