Walker signed the bills Friday. They had passed the Senate and Assembly unanimously.
The pay raises will be applied retroactively to June 30.
Non-union state workers, the vast majority of the 69,000 state employees, received the same 1 percent raise under the budget that took effect in July.
Most bargaining units decided not to negotiate since the 2011 law known as Act 10 limited bargaining to just base pay increases no greater than inflation.
The five unions represent all state education professionals, all classified attorneys, nurses, electricians, and others represented by the building and trades bargaining unit, research analysts and economists.